src/Pure/Tools/update_imports.scala

     selected.flatMap(session_name =>
     {
       val info = full_sessions(session_name)
       val session_base = deps(session_name)
       val resources = new Resources(session_base)
-      val local_theories = session_base.known.theories_local.iterator.map(_._2).toSet
+      val local_theories =
+        (for {
+          (_, name) <- session_base.known.theories_local.iterator
+          if resources.theory_qualifier(name) == info.theory_qualifier
+        } yield name).toSet
 
       def standard_import(qualifier: String, dir: String, s: String): String =
       {
         val name = resources.import_name(qualifier, dir, s)
         if (!local_theories.contains(name)) s