diff -r 05c680ebf512 -r 873f638fd7db mercurial/merge.py
--- a/mercurial/merge.py	Sun Jun 25 17:00:15 2017 -0700
+++ b/mercurial/merge.py	Sun Jun 25 22:29:09 2017 -0700
@@ -1291,7 +1291,7 @@
         progress(_updating, z, item=f, total=numupdates, unit=_files)
         flags, = args
         audit(f)
-        repo.wvfs.setflags(f, 'l' in flags, 'x' in flags)
+        wctx[f].setflags('l' in flags, 'x' in flags)
         updated += 1
 
     # the ordering is important here -- ms.mergedriver will raise if the merge