--- a/mercurial/localrepo.py
+++ b/mercurial/localrepo.py
@@ -810,6 +810,8 @@ class localrepository(repo.repository):
if f in m1:
del m1[f]
removed.append(f)
+ elif f in m2:
+ removed.append(f)
mn = self.manifest.add(m1, tr, linkrev, c1[0], c2[0], (new, removed))
# add changeset