diff --git a/mercurial/config.py b/mercurial/config.py
--- a/mercurial/config.py
+++ b/mercurial/config.py
@@ -108,6 +108,16 @@
             self._source = self._source.preparewrite()
             self._source[(section, item)] = source
 
+    def alter(self, section, key, new_value):
+        """alter a value without altering its source or level
+
+        This method is meant to be used by `ui.fixconfig` only."""
+        item = self._data[section][key]
+        size = len(item)
+        new_item = (new_value,) + item[1:]
+        assert len(new_item) == size
+        self._data[section][key] = new_item
+
     def restore(self, data):
         """restore data returned by self.backup"""
         self._source = self._source.preparewrite()
diff --git a/mercurial/ui.py b/mercurial/ui.py
--- a/mercurial/ui.py
+++ b/mercurial/ui.py
@@ -554,7 +554,7 @@
                     p = util.expandpath(p)
                     if not util.hasscheme(p) and not os.path.isabs(p):
                         p = os.path.normpath(os.path.join(root, p))
-                    c.set(b"paths", n, p)
+                    c.alter(b"paths", n, p)
 
         if section in (None, b'ui'):
             # update ui options