diff -r 1b7d907ec18a -r ee935a6e1ea2 mercurial/localrepo.py
--- a/mercurial/localrepo.py	Thu May 12 22:29:05 2016 -0400
+++ b/mercurial/localrepo.py	Wed May 25 15:32:35 2016 -0500
@@ -1388,6 +1388,8 @@
             node = fctx.filenode()
             if node in [fparent1, fparent2]:
                 self.ui.debug('reusing %s filelog entry\n' % fname)
+                if manifest1.flags(fname) != fctx.flags():
+                    changelist.append(fname)
                 return node
 
         flog = self.file(fname)