diff --git a/Godeps/Godeps.json b/Godeps/Godeps.json
index 15857ef0..1886f33d 100644
--- a/Godeps/Godeps.json
+++ b/Godeps/Godeps.json
@@ -31,7 +31,7 @@
 		},
 		{
 			"ImportPath": "github.com/syncthing/protocol",
-			"Rev": "3d8a71fdb205fe2401a341a739208bc9d1e79a1b"
+			"Rev": "e7db2648034fb71b051902a02bc25d4468ed492e"
 		},
 		{
 			"ImportPath": "github.com/syndtr/goleveldb/leveldb",
diff --git a/Godeps/_workspace/src/github.com/syncthing/protocol/vector.go b/Godeps/_workspace/src/github.com/syncthing/protocol/vector.go
index 04859452..edd15614 100644
--- a/Godeps/_workspace/src/github.com/syncthing/protocol/vector.go
+++ b/Godeps/_workspace/src/github.com/syncthing/protocol/vector.go
@@ -103,3 +103,13 @@ func (a Vector) Concurrent(b Vector) bool {
 	comp := a.Compare(b)
 	return comp == ConcurrentGreater || comp == ConcurrentLesser
 }
+
+// Counter returns the current value of the given counter ID.
+func (v Vector) Counter(id uint64) uint64 {
+	for _, c := range v {
+		if c.ID == id {
+			return c.Value
+		}
+	}
+	return 0
+}
diff --git a/Godeps/_workspace/src/github.com/syncthing/protocol/vector_test.go b/Godeps/_workspace/src/github.com/syncthing/protocol/vector_test.go
index 7815412c..c01255e7 100644
--- a/Godeps/_workspace/src/github.com/syncthing/protocol/vector_test.go
+++ b/Godeps/_workspace/src/github.com/syncthing/protocol/vector_test.go
@@ -118,5 +118,17 @@ func TestMerge(t *testing.T) {
 			t.Errorf("%d: %+v.Merge(%+v) == %+v (expected %+v)", i, tc.a, tc.b, m, tc.m)
 		}
 	}
-
+}
+
+func TestCounterValue(t *testing.T) {
+	v0 := Vector{Counter{42, 1}, Counter{64, 5}}
+	if v0.Counter(42) != 1 {
+		t.Error("Counter error, %d != %d", v0.Counter(42), 1)
+	}
+	if v0.Counter(64) != 5 {
+		t.Error("Counter error, %d != %d", v0.Counter(64), 5)
+	}
+	if v0.Counter(72) != 0 {
+		t.Error("Counter error, %d != %d", v0.Counter(72), 0)
+	}
 }
diff --git a/Godeps/_workspace/src/github.com/thejerf/suture/pre-commit b/Godeps/_workspace/src/github.com/thejerf/suture/pre-commit
index c88ec0fe..6199d610 100644
--- a/Godeps/_workspace/src/github.com/thejerf/suture/pre-commit
+++ b/Godeps/_workspace/src/github.com/thejerf/suture/pre-commit
@@ -9,3 +9,4 @@ if [ ! -z "$GOLINTOUT" -o "$?" != 0 ]; then
 fi
 
 go test
+
diff --git a/internal/model/model.go b/internal/model/model.go
index fa122d8a..7965fca3 100644
--- a/internal/model/model.go
+++ b/internal/model/model.go
@@ -142,7 +142,7 @@ func (m *Model) StartFolderRW(folder string) {
 	if ok {
 		panic("cannot start already running folder " + folder)
 	}
-	p := newRWFolder(m, cfg)
+	p := newRWFolder(m, m.shortID, cfg)
 	m.folderRunners[folder] = p
 	m.fmut.Unlock()
 
diff --git a/internal/model/rwfolder.go b/internal/model/rwfolder.go
index 97108165..25eafcf5 100644
--- a/internal/model/rwfolder.go
+++ b/internal/model/rwfolder.go
@@ -68,13 +68,14 @@ type rwFolder struct {
 	lenientMtimes bool
 	copiers       int
 	pullers       int
+	shortID       uint64
 
 	stop      chan struct{}
 	queue     *jobQueue
 	dbUpdates chan protocol.FileInfo
 }
 
-func newRWFolder(m *Model, cfg config.FolderConfiguration) *rwFolder {
+func newRWFolder(m *Model, shortID uint64, cfg config.FolderConfiguration) *rwFolder {
 	return &rwFolder{
 		stateTracker: stateTracker{folder: cfg.ID},
 
@@ -88,6 +89,7 @@ func newRWFolder(m *Model, cfg config.FolderConfiguration) *rwFolder {
 		lenientMtimes: cfg.LenientMtimes,
 		copiers:       cfg.Copiers,
 		pullers:       cfg.Pullers,
+		shortID:       shortID,
 
 		stop:  make(chan struct{}),
 		queue: newJobQueue(),
@@ -603,8 +605,11 @@ func (p *rwFolder) deleteFile(file protocol.FileInfo) {
 	realName := filepath.Join(p.dir, file.Name)
 
 	cur, ok := p.model.CurrentFolderFile(p.folder, file.Name)
-	if ok && cur.Version.Concurrent(file.Version) {
-		// There is a conflict here. Move the file to a conflict copy instead of deleting.
+	if ok && p.inConflict(cur.Version, file.Version) {
+		// There is a conflict here. Move the file to a conflict copy instead
+		// of deleting. Also merge with the version vector we had, to indicate
+		// we have resolved the conflict.
+		file.Version = file.Version.Merge(cur.Version)
 		err = osutil.InWritableDir(moveForConflict, realName)
 	} else if p.versioner != nil {
 		err = osutil.InWritableDir(p.versioner.Archive, realName)
@@ -816,6 +821,12 @@ func (p *rwFolder) shortcutFile(file protocol.FileInfo) (err error) {
 		}
 	}
 
+	// This may have been a conflict. We should merge the version vectors so
+	// that our clock doesn't move backwards.
+	if cur, ok := p.model.CurrentFolderFile(p.folder, file.Name); ok {
+		file.Version = file.Version.Merge(cur.Version)
+	}
+
 	p.dbUpdates <- file
 	return
 }
@@ -1011,10 +1022,12 @@ func (p *rwFolder) performFinish(state *sharedPullerState) {
 		}
 	}
 
-	if state.version.Concurrent(state.file.Version) {
+	if p.inConflict(state.version, state.file.Version) {
 		// The new file has been changed in conflict with the existing one. We
 		// should file it away as a conflict instead of just removing or
-		// archiving.
+		// archiving. Also merge with the version vector we had, to indicate
+		// we have resolved the conflict.
+		state.file.Version = state.file.Version.Merge(state.version)
 		err = osutil.InWritableDir(moveForConflict, state.realName)
 	} else if p.versioner != nil {
 		// If we should use versioning, let the versioner archive the old
@@ -1144,6 +1157,22 @@ loop:
 	}
 }
 
+func (p *rwFolder) inConflict(current, replacement protocol.Vector) bool {
+	if current.Concurrent(replacement) {
+		// Obvious case
+		return true
+	}
+	if replacement.Counter(p.shortID) > current.Counter(p.shortID) {
+		// The replacement file contains a higher version for ourselves than
+		// what we have. This isn't supposed to be possible, since it's only
+		// we who can increment that counter. We take it as a sign that
+		// something is wrong (our index may have been corrupted or removed)
+		// and flag it as a conflict.
+		return true
+	}
+	return false
+}
+
 func invalidateFolder(cfg *config.Configuration, folderID string, err error) {
 	for i := range cfg.Folders {
 		folder := &cfg.Folders[i]