diff --git a/mercurial/merge.py b/mercurial/merge.py
--- a/mercurial/merge.py
+++ b/mercurial/merge.py
@@ -1288,7 +1288,7 @@ def applyupdates(repo, actions, wctx, mc
         progress(_updating, z, item=f, total=numupdates, unit=_files)
         flags, = args
         audit(f)
-        util.setflags(repo.wjoin(f), 'l' in flags, 'x' in flags)
+        repo.wvfs.setflags(f, 'l' in flags, 'x' in flags)
         updated += 1
 
     # the ordering is important here -- ms.mergedriver will raise if the merge