diff -r 2efdd186925d -r f49d60fa40a5 mercurial/repair.py
--- a/mercurial/repair.py	Mon Mar 24 15:35:07 2014 -0700
+++ b/mercurial/repair.py	Mon Mar 24 15:43:15 2014 -0700
@@ -134,6 +134,8 @@
             for i in xrange(offset, len(tr.entries)):
                 file, troffset, ignore = tr.entries[i]
                 repo.sopener(file, 'a').truncate(troffset)
+                if troffset == 0:
+                    repo.store.markremoved(file)
             tr.close()
         except: # re-raises
             tr.abort()