diff --git a/src/cmds/restic/cmd_prune.go b/src/cmds/restic/cmd_prune.go
index 17ccdc813..d2a77be24 100644
--- a/src/cmds/restic/cmd_prune.go
+++ b/src/cmds/restic/cmd_prune.go
@@ -106,7 +106,7 @@ func pruneRepository(gopts GlobalOptions, repo restic.Repository) error {
 	Verbosef("building new index for repo\n")
 
 	bar := newProgressMax(!gopts.Quiet, uint64(stats.packs), "packs")
-	idx, err := index.New(ctx, repo, bar)
+	idx, err := index.New(ctx, repo, restic.NewIDSet(), bar)
 	if err != nil {
 		return err
 	}
@@ -161,6 +161,10 @@ func pruneRepository(gopts GlobalOptions, repo restic.Repository) error {
 
 		err = restic.FindUsedBlobs(ctx, repo, *sn.Tree, usedBlobs, seenBlobs)
 		if err != nil {
+			if repo.Backend().IsNotExist(err) {
+				return errors.Fatal("unable to load a tree from the repo: " + err.Error())
+			}
+
 			return err
 		}
 
@@ -221,16 +225,22 @@ func pruneRepository(gopts GlobalOptions, repo restic.Repository) error {
 	Verbosef("will delete %d packs and rewrite %d packs, this frees %s\n",
 		len(removePacks), len(rewritePacks), formatBytes(uint64(removeBytes)))
 
+	var repackedBlobs restic.IDSet
 	if len(rewritePacks) != 0 {
 		bar = newProgressMax(!gopts.Quiet, uint64(len(rewritePacks)), "packs rewritten")
 		bar.Start()
-		err = repository.Repack(ctx, repo, rewritePacks, usedBlobs, bar)
+		repackedBlobs, err = repository.Repack(ctx, repo, rewritePacks, usedBlobs, bar)
 		if err != nil {
 			return err
 		}
 		bar.Done()
 	}
 
+	if err = rebuildIndex(ctx, repo, removePacks); err != nil {
+		return err
+	}
+
+	removePacks.Merge(repackedBlobs)
 	if len(removePacks) != 0 {
 		bar = newProgressMax(!gopts.Quiet, uint64(len(removePacks)), "packs deleted")
 		bar.Start()
@@ -245,10 +255,6 @@ func pruneRepository(gopts GlobalOptions, repo restic.Repository) error {
 		bar.Done()
 	}
 
-	if err = rebuildIndex(ctx, repo); err != nil {
-		return err
-	}
-
 	Verbosef("done\n")
 	return nil
 }
diff --git a/src/cmds/restic/cmd_rebuild_index.go b/src/cmds/restic/cmd_rebuild_index.go
index 6a60ea900..9f3cc888c 100644
--- a/src/cmds/restic/cmd_rebuild_index.go
+++ b/src/cmds/restic/cmd_rebuild_index.go
@@ -38,10 +38,10 @@ func runRebuildIndex(gopts GlobalOptions) error {
 
 	ctx, cancel := context.WithCancel(gopts.ctx)
 	defer cancel()
-	return rebuildIndex(ctx, repo)
+	return rebuildIndex(ctx, repo, restic.NewIDSet())
 }
 
-func rebuildIndex(ctx context.Context, repo restic.Repository) error {
+func rebuildIndex(ctx context.Context, repo restic.Repository, ignorePacks restic.IDSet) error {
 	Verbosef("counting files in repo\n")
 
 	var packs uint64
@@ -50,7 +50,7 @@ func rebuildIndex(ctx context.Context, repo restic.Repository) error {
 	}
 
 	bar := newProgressMax(!globalOptions.Quiet, packs, "packs")
-	idx, err := index.New(ctx, repo, bar)
+	idx, err := index.New(ctx, repo, ignorePacks, bar)
 	if err != nil {
 		return err
 	}
diff --git a/src/restic/backend.go b/src/restic/backend.go
index 0020a76a9..b3d91cc62 100644
--- a/src/restic/backend.go
+++ b/src/restic/backend.go
@@ -36,6 +36,10 @@ type Backend interface {
 	// arbitrary order. A goroutine is started for this, which is stopped when
 	// ctx is cancelled.
 	List(ctx context.Context, t FileType) <-chan string
+
+	// IsNotExist returns true if the error was caused by a non-existing file
+	// in the backend.
+	IsNotExist(err error) bool
 }
 
 // FileInfo is returned by Stat() and contains information about a file in the
diff --git a/src/restic/backend/b2/b2.go b/src/restic/backend/b2/b2.go
index c19915038..69ccb9bdc 100644
--- a/src/restic/backend/b2/b2.go
+++ b/src/restic/backend/b2/b2.go
@@ -151,6 +151,11 @@ func (wr *wrapReader) Close() error {
 	return err
 }
 
+// IsNotExist returns true if the error is caused by a non-existing file.
+func (be *b2Backend) IsNotExist(err error) bool {
+	return b2.IsNotExist(errors.Cause(err))
+}
+
 // Load returns the data stored in the backend for h at the given offset
 // and saves it in p. Load has the same semantics as io.ReaderAt.
 func (be *b2Backend) Load(ctx context.Context, h restic.Handle, length int, offset int64) (io.ReadCloser, error) {
diff --git a/src/restic/backend/local/local.go b/src/restic/backend/local/local.go
index 1a3c0158c..4d58b187d 100644
--- a/src/restic/backend/local/local.go
+++ b/src/restic/backend/local/local.go
@@ -75,6 +75,11 @@ func (b *Local) Location() string {
 	return b.Path
 }
 
+// IsNotExist returns true if the error is caused by a non existing file.
+func (b *Local) IsNotExist(err error) bool {
+	return os.IsNotExist(errors.Cause(err))
+}
+
 // Save stores data in the backend at the handle.
 func (b *Local) Save(ctx context.Context, h restic.Handle, rd io.Reader) (err error) {
 	debug.Log("Save %v", h)
diff --git a/src/restic/backend/mem/mem_backend.go b/src/restic/backend/mem/mem_backend.go
index bbb4dbd1a..cee81799a 100644
--- a/src/restic/backend/mem/mem_backend.go
+++ b/src/restic/backend/mem/mem_backend.go
@@ -19,6 +19,8 @@ type memMap map[restic.Handle][]byte
 // make sure that MemoryBackend implements backend.Backend
 var _ restic.Backend = &MemoryBackend{}
 
+var errNotFound = errors.New("not found")
+
 // MemoryBackend is a mock backend that uses a map for storing all data in
 // memory. This should only be used for tests.
 type MemoryBackend struct {
@@ -51,6 +53,11 @@ func (be *MemoryBackend) Test(ctx context.Context, h restic.Handle) (bool, error
 	return false, nil
 }
 
+// IsNotExist returns true if the file does not exist.
+func (be *MemoryBackend) IsNotExist(err error) bool {
+	return errors.Cause(err) == errNotFound
+}
+
 // Save adds new Data to the backend.
 func (be *MemoryBackend) Save(ctx context.Context, h restic.Handle, rd io.Reader) error {
 	if err := h.Valid(); err != nil {
@@ -101,7 +108,7 @@ func (be *MemoryBackend) Load(ctx context.Context, h restic.Handle, length int,
 	}
 
 	if _, ok := be.data[h]; !ok {
-		return nil, errors.New("no such data")
+		return nil, errNotFound
 	}
 
 	buf := be.data[h]
@@ -134,7 +141,7 @@ func (be *MemoryBackend) Stat(ctx context.Context, h restic.Handle) (restic.File
 
 	e, ok := be.data[h]
 	if !ok {
-		return restic.FileInfo{}, errors.New("no such data")
+		return restic.FileInfo{}, errNotFound
 	}
 
 	return restic.FileInfo{Size: int64(len(e))}, nil
@@ -148,7 +155,7 @@ func (be *MemoryBackend) Remove(ctx context.Context, h restic.Handle) error {
 	debug.Log("Remove %v", h)
 
 	if _, ok := be.data[h]; !ok {
-		return errors.New("no such data")
+		return errNotFound
 	}
 
 	delete(be.data, h)
diff --git a/src/restic/backend/rest/rest.go b/src/restic/backend/rest/rest.go
index 4145a2a32..99dc2ba63 100644
--- a/src/restic/backend/rest/rest.go
+++ b/src/restic/backend/rest/rest.go
@@ -138,6 +138,23 @@ func (b *restBackend) Save(ctx context.Context, h restic.Handle, rd io.Reader) (
 	return nil
 }
 
+// ErrIsNotExist is returned whenever the requested file does not exist on the
+// server.
+type ErrIsNotExist struct {
+	restic.Handle
+}
+
+func (e ErrIsNotExist) Error() string {
+	return fmt.Sprintf("%v does not exist", e.Handle)
+}
+
+// IsNotExist returns true if the error was caused by a non-existing file.
+func (b *restBackend) IsNotExist(err error) bool {
+	err = errors.Cause(err)
+	_, ok := err.(ErrIsNotExist)
+	return ok
+}
+
 // Load returns a reader that yields the contents of the file at h at the
 // given offset. If length is nonzero, only a portion of the file is
 // returned. rd must be closed after use.
@@ -179,6 +196,11 @@ func (b *restBackend) Load(ctx context.Context, h restic.Handle, length int, off
 		return nil, errors.Wrap(err, "client.Do")
 	}
 
+	if resp.StatusCode == http.StatusNotFound {
+		_ = resp.Body.Close()
+		return nil, ErrIsNotExist{h}
+	}
+
 	if resp.StatusCode != 200 && resp.StatusCode != 206 {
 		_ = resp.Body.Close()
 		return nil, errors.Errorf("unexpected HTTP response (%v): %v", resp.StatusCode, resp.Status)
@@ -205,6 +227,11 @@ func (b *restBackend) Stat(ctx context.Context, h restic.Handle) (restic.FileInf
 		return restic.FileInfo{}, errors.Wrap(err, "Close")
 	}
 
+	if resp.StatusCode == http.StatusNotFound {
+		_ = resp.Body.Close()
+		return restic.FileInfo{}, ErrIsNotExist{h}
+	}
+
 	if resp.StatusCode != 200 {
 		return restic.FileInfo{}, errors.Errorf("unexpected HTTP response (%v): %v", resp.StatusCode, resp.Status)
 	}
@@ -248,6 +275,11 @@ func (b *restBackend) Remove(ctx context.Context, h restic.Handle) error {
 		return errors.Wrap(err, "client.Do")
 	}
 
+	if resp.StatusCode == http.StatusNotFound {
+		_ = resp.Body.Close()
+		return ErrIsNotExist{h}
+	}
+
 	if resp.StatusCode != 200 {
 		return errors.Errorf("blob not removed, server response: %v (%v)", resp.Status, resp.StatusCode)
 	}
diff --git a/src/restic/index/index.go b/src/restic/index/index.go
index ab1ebafa4..be528efc0 100644
--- a/src/restic/index/index.go
+++ b/src/restic/index/index.go
@@ -34,12 +34,12 @@ func newIndex() *Index {
 }
 
 // New creates a new index for repo from scratch.
-func New(ctx context.Context, repo restic.Repository, p *restic.Progress) (*Index, error) {
+func New(ctx context.Context, repo restic.Repository, ignorePacks restic.IDSet, p *restic.Progress) (*Index, error) {
 	p.Start()
 	defer p.Done()
 
 	ch := make(chan worker.Job)
-	go list.AllPacks(ctx, repo, ch)
+	go list.AllPacks(ctx, repo, ignorePacks, ch)
 
 	idx := newIndex()
 
diff --git a/src/restic/index/index_test.go b/src/restic/index/index_test.go
index 11d0cc08a..81c3d6e4b 100644
--- a/src/restic/index/index_test.go
+++ b/src/restic/index/index_test.go
@@ -43,7 +43,7 @@ func TestIndexNew(t *testing.T) {
 	repo, cleanup := createFilledRepo(t, 3, 0)
 	defer cleanup()
 
-	idx, err := New(context.TODO(), repo, nil)
+	idx, err := New(context.TODO(), repo, restic.NewIDSet(), nil)
 	if err != nil {
 		t.Fatalf("New() returned error %v", err)
 	}
@@ -70,7 +70,7 @@ func TestIndexLoad(t *testing.T) {
 
 	validateIndex(t, repo, loadIdx)
 
-	newIdx, err := New(context.TODO(), repo, nil)
+	newIdx, err := New(context.TODO(), repo, restic.NewIDSet(), nil)
 	if err != nil {
 		t.Fatalf("New() returned error %v", err)
 	}
@@ -134,7 +134,7 @@ func BenchmarkIndexNew(b *testing.B) {
 	b.ResetTimer()
 
 	for i := 0; i < b.N; i++ {
-		idx, err := New(context.TODO(), repo, nil)
+		idx, err := New(context.TODO(), repo, restic.NewIDSet(), nil)
 
 		if err != nil {
 			b.Fatalf("New() returned error %v", err)
@@ -151,7 +151,7 @@ func BenchmarkIndexSave(b *testing.B) {
 	repo, cleanup := repository.TestRepository(b)
 	defer cleanup()
 
-	idx, err := New(context.TODO(), repo, nil)
+	idx, err := New(context.TODO(), repo, restic.NewIDSet(), nil)
 	test.OK(b, err)
 
 	for i := 0; i < 8000; i++ {
@@ -184,7 +184,7 @@ func TestIndexDuplicateBlobs(t *testing.T) {
 	repo, cleanup := createFilledRepo(t, 3, 0.01)
 	defer cleanup()
 
-	idx, err := New(context.TODO(), repo, nil)
+	idx, err := New(context.TODO(), repo, restic.NewIDSet(), nil)
 	if err != nil {
 		t.Fatal(err)
 	}
diff --git a/src/restic/list/list.go b/src/restic/list/list.go
index 292ba8475..6bd9d23aa 100644
--- a/src/restic/list/list.go
+++ b/src/restic/list/list.go
@@ -37,7 +37,7 @@ func (l Result) Entries() []restic.Blob {
 }
 
 // AllPacks sends the contents of all packs to ch.
-func AllPacks(ctx context.Context, repo Lister, ch chan<- worker.Job) {
+func AllPacks(ctx context.Context, repo Lister, ignorePacks restic.IDSet, ch chan<- worker.Job) {
 	f := func(ctx context.Context, job worker.Job) (interface{}, error) {
 		packID := job.Data.(restic.ID)
 		entries, size, err := repo.ListPack(ctx, packID)
@@ -55,6 +55,10 @@ func AllPacks(ctx context.Context, repo Lister, ch chan<- worker.Job) {
 	go func() {
 		defer close(jobCh)
 		for id := range repo.List(ctx, restic.DataFile) {
+			if ignorePacks.Has(id) {
+				continue
+			}
+
 			select {
 			case jobCh <- worker.Job{Data: id}:
 			case <-ctx.Done():
diff --git a/src/restic/mock/backend.go b/src/restic/mock/backend.go
index 10effe045..ead50efcb 100644
--- a/src/restic/mock/backend.go
+++ b/src/restic/mock/backend.go
@@ -10,15 +10,16 @@ import (
 
 // Backend implements a mock backend.
 type Backend struct {
-	CloseFn    func() error
-	SaveFn     func(ctx context.Context, h restic.Handle, rd io.Reader) error
-	LoadFn     func(ctx context.Context, h restic.Handle, length int, offset int64) (io.ReadCloser, error)
-	StatFn     func(ctx context.Context, h restic.Handle) (restic.FileInfo, error)
-	ListFn     func(ctx context.Context, t restic.FileType) <-chan string
-	RemoveFn   func(ctx context.Context, h restic.Handle) error
-	TestFn     func(ctx context.Context, h restic.Handle) (bool, error)
-	DeleteFn   func(ctx context.Context) error
-	LocationFn func() string
+	CloseFn      func() error
+	IsNotExistFn func(err error) bool
+	SaveFn       func(ctx context.Context, h restic.Handle, rd io.Reader) error
+	LoadFn       func(ctx context.Context, h restic.Handle, length int, offset int64) (io.ReadCloser, error)
+	StatFn       func(ctx context.Context, h restic.Handle) (restic.FileInfo, error)
+	ListFn       func(ctx context.Context, t restic.FileType) <-chan string
+	RemoveFn     func(ctx context.Context, h restic.Handle) error
+	TestFn       func(ctx context.Context, h restic.Handle) (bool, error)
+	DeleteFn     func(ctx context.Context) error
+	LocationFn   func() string
 }
 
 // Close the backend.
@@ -39,6 +40,15 @@ func (m *Backend) Location() string {
 	return m.LocationFn()
 }
 
+// IsNotExist returns true if the error is caused by a missing file.
+func (m *Backend) IsNotExist(err error) bool {
+	if m.IsNotExistFn == nil {
+		return false
+	}
+
+	return m.IsNotExistFn(err)
+}
+
 // Save data in the backend.
 func (m *Backend) Save(ctx context.Context, h restic.Handle, rd io.Reader) error {
 	if m.SaveFn == nil {
diff --git a/src/restic/repository/repack.go b/src/restic/repository/repack.go
index 36a000783..e613d8da2 100644
--- a/src/restic/repository/repack.go
+++ b/src/restic/repository/repack.go
@@ -16,9 +16,9 @@ import (
 
 // Repack takes a list of packs together with a list of blobs contained in
 // these packs. Each pack is loaded and the blobs listed in keepBlobs is saved
-// into a new pack. Afterwards, the packs are removed. This operation requires
-// an exclusive lock on the repo.
-func Repack(ctx context.Context, repo restic.Repository, packs restic.IDSet, keepBlobs restic.BlobSet, p *restic.Progress) (err error) {
+// into a new pack. Returned is the list of obsolete packs which can then
+// be removed.
+func Repack(ctx context.Context, repo restic.Repository, packs restic.IDSet, keepBlobs restic.BlobSet, p *restic.Progress) (obsoletePacks restic.IDSet, err error) {
 	debug.Log("repacking %d packs while keeping %d blobs", len(packs), len(keepBlobs))
 
 	for packID := range packs {
@@ -27,39 +27,39 @@ func Repack(ctx context.Context, repo restic.Repository, packs restic.IDSet, kee
 
 		tempfile, err := fs.TempFile("", "restic-temp-repack-")
 		if err != nil {
-			return errors.Wrap(err, "TempFile")
+			return nil, errors.Wrap(err, "TempFile")
 		}
 
 		beRd, err := repo.Backend().Load(ctx, h, 0, 0)
 		if err != nil {
-			return err
+			return nil, err
 		}
 
 		hrd := hashing.NewReader(beRd, sha256.New())
 		packLength, err := io.Copy(tempfile, hrd)
 		if err != nil {
-			return errors.Wrap(err, "Copy")
+			return nil, errors.Wrap(err, "Copy")
 		}
 
 		if err = beRd.Close(); err != nil {
-			return errors.Wrap(err, "Close")
+			return nil, errors.Wrap(err, "Close")
 		}
 
 		hash := restic.IDFromHash(hrd.Sum(nil))
 		debug.Log("pack %v loaded (%d bytes), hash %v", packID.Str(), packLength, hash.Str())
 
 		if !packID.Equal(hash) {
-			return errors.Errorf("hash does not match id: want %v, got %v", packID, hash)
+			return nil, errors.Errorf("hash does not match id: want %v, got %v", packID, hash)
 		}
 
 		_, err = tempfile.Seek(0, 0)
 		if err != nil {
-			return errors.Wrap(err, "Seek")
+			return nil, errors.Wrap(err, "Seek")
 		}
 
 		blobs, err := pack.List(repo.Key(), tempfile, packLength)
 		if err != nil {
-			return err
+			return nil, err
 		}
 
 		debug.Log("processing pack %v, blobs: %v", packID.Str(), len(blobs))
@@ -80,30 +80,30 @@ func Repack(ctx context.Context, repo restic.Repository, packs restic.IDSet, kee
 
 			n, err := tempfile.ReadAt(buf, int64(entry.Offset))
 			if err != nil {
-				return errors.Wrap(err, "ReadAt")
+				return nil, errors.Wrap(err, "ReadAt")
 			}
 
 			if n != len(buf) {
-				return errors.Errorf("read blob %v from %v: not enough bytes read, want %v, got %v",
+				return nil, errors.Errorf("read blob %v from %v: not enough bytes read, want %v, got %v",
 					h, tempfile.Name(), len(buf), n)
 			}
 
 			n, err = crypto.Decrypt(repo.Key(), buf, buf)
 			if err != nil {
-				return err
+				return nil, err
 			}
 
 			buf = buf[:n]
 
 			id := restic.Hash(buf)
 			if !id.Equal(entry.ID) {
-				return errors.Errorf("read blob %v from %v: wrong data returned, hash is %v",
+				return nil, errors.Errorf("read blob %v from %v: wrong data returned, hash is %v",
 					h, tempfile.Name(), id)
 			}
 
 			_, err = repo.SaveBlob(ctx, entry.Type, buf, entry.ID)
 			if err != nil {
-				return err
+				return nil, err
 			}
 
 			debug.Log("  saved blob %v", entry.ID.Str())
@@ -112,11 +112,11 @@ func Repack(ctx context.Context, repo restic.Repository, packs restic.IDSet, kee
 		}
 
 		if err = tempfile.Close(); err != nil {
-			return errors.Wrap(err, "Close")
+			return nil, errors.Wrap(err, "Close")
 		}
 
 		if err = fs.RemoveIfExists(tempfile.Name()); err != nil {
-			return errors.Wrap(err, "Remove")
+			return nil, errors.Wrap(err, "Remove")
 		}
 		if p != nil {
 			p.Report(restic.Stat{Blobs: 1})
@@ -124,18 +124,8 @@ func Repack(ctx context.Context, repo restic.Repository, packs restic.IDSet, kee
 	}
 
 	if err := repo.Flush(); err != nil {
-		return err
+		return nil, err
 	}
 
-	for packID := range packs {
-		h := restic.Handle{Type: restic.DataFile, Name: packID.String()}
-		err := repo.Backend().Remove(ctx, h)
-		if err != nil {
-			debug.Log("error removing pack %v: %v", packID.Str(), err)
-			return err
-		}
-		debug.Log("removed pack %v", packID.Str())
-	}
-
-	return nil
+	return packs, nil
 }
diff --git a/src/restic/repository/repack_test.go b/src/restic/repository/repack_test.go
index d339cf2b8..fa64f8eff 100644
--- a/src/restic/repository/repack_test.go
+++ b/src/restic/repository/repack_test.go
@@ -127,10 +127,17 @@ func findPacksForBlobs(t *testing.T, repo restic.Repository, blobs restic.BlobSe
 }
 
 func repack(t *testing.T, repo restic.Repository, packs restic.IDSet, blobs restic.BlobSet) {
-	err := repository.Repack(context.TODO(), repo, packs, blobs, nil)
+	repackedBlobs, err := repository.Repack(context.TODO(), repo, packs, blobs, nil)
 	if err != nil {
 		t.Fatal(err)
 	}
+
+	for id := range repackedBlobs {
+		err = repo.Backend().Remove(context.TODO(), restic.Handle{Type: restic.DataFile, Name: id.String()})
+		if err != nil {
+			t.Fatal(err)
+		}
+	}
 }
 
 func saveIndex(t *testing.T, repo restic.Repository) {
@@ -140,7 +147,7 @@ func saveIndex(t *testing.T, repo restic.Repository) {
 }
 
 func rebuildIndex(t *testing.T, repo restic.Repository) {
-	idx, err := index.New(context.TODO(), repo, nil)
+	idx, err := index.New(context.TODO(), repo, restic.NewIDSet(), nil)
 	if err != nil {
 		t.Fatal(err)
 	}