diff --git a/project.py b/project.py
index 0da2118b9..1c85b0445 100644
--- a/project.py
+++ b/project.py
@@ -1462,6 +1462,8 @@ def _dosubmodules():
         cnt_mine += 1
 
     if not upstream_gain and cnt_mine == len(local_changes):
+      # The copy/linkfile config may have changed.
+      self._CopyAndLinkFiles()
       return
 
     if self.IsDirty(consider_untracked=False):