diff --git a/project.py b/project.py
index 9e05a96..437edca 100644
--- a/project.py
+++ b/project.py
@@ -1235,7 +1235,9 @@
         old_copylink = fd.read().split('\n')
       finally:
         fd.close()
-    for target in old_copylink:
+    for dest in old_copylink:
+      if not dest: continue
+      target = os.path.join(self.manifest.topdir, dest)
       if os.path.exists(target):
         if IsTrace():
           Trace('rm %s', target)
@@ -1248,10 +1250,10 @@
     new_copylink = []
     for copyfile in self.copyfiles:
       copyfile._Copy()
-      new_copylink.append(copyfile.abs_dest)
+      new_copylink.append(copyfile.dest)
     for linkfile in self.linkfiles:
       linkfile._Link()
-      new_copylink.append(linkfile.abs_dest)
+      new_copylink.append(linkfile.dest)
     file_path = os.path.join(self.gitdir, '.repo_copylink')
     fd = open(file_path, 'w')
     try: