diff --git a/mercurial/context.py b/mercurial/context.py
--- a/mercurial/context.py
+++ b/mercurial/context.py
@@ -1896,6 +1896,9 @@ class workingfilectx(committablefilectx)
         """wraps repo.wwrite"""
         self._repo.wwrite(self._path, data, flags)
 
+    def setflags(self, l, x):
+        self._repo.wvfs.setflags(self._path, l, x)
+
 class workingcommitctx(workingctx):
     """A workingcommitctx object makes access to data related to
     the revision being committed convenient.
diff --git a/mercurial/merge.py b/mercurial/merge.py
--- a/mercurial/merge.py
+++ b/mercurial/merge.py
@@ -1291,7 +1291,7 @@ def applyupdates(repo, actions, wctx, mc
         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