diff --git a/mercurial/localrepo.py b/mercurial/localrepo.py
--- a/mercurial/localrepo.py
+++ b/mercurial/localrepo.py
@@ -1420,10 +1420,11 @@ class localrepository(repo.repository):
                 mf2 = mfmatches(ctx2)
 
             modified, added, clean = [], [], []
+            withflags = mf1.withflags() | mf2.withflags()
             for fn in mf2:
                 if fn in mf1:
                     if (fn not in deleted and
-                        (mf1.flags(fn) != mf2.flags(fn) or
+                        ((fn in withflags and mf1.flags(fn) != mf2.flags(fn)) or
                          (mf1[fn] != mf2[fn] and
                           (mf2[fn] or ctx1[fn].cmp(ctx2[fn]))))):
                         modified.append(fn)
diff --git a/mercurial/manifest.py b/mercurial/manifest.py
--- a/mercurial/manifest.py
+++ b/mercurial/manifest.py
@@ -19,6 +19,8 @@ class manifestdict(dict):
         self._flags = flags
     def flags(self, f):
         return self._flags.get(f, "")
+    def withflags(self):
+        return set(self._flags.keys())
     def set(self, f, flags):
         self._flags[f] = flags
     def copy(self):