diff --git a/src/base_media_func.h b/src/base_media_func.h
--- a/src/base_media_func.h
+++ b/src/base_media_func.h
@@ -159,6 +159,11 @@ bool BaseMedia<Tbase_set>::AddFile(const
 				/* don't allow recursive delete of all remaining items */
 				duplicate->next = NULL;
 
+				/* If the duplicate set is currently used (due to rescanning this can happen)
+				 * update the currently used set to the new one. This will 'lie' about the
+				 * version number until a new game is started which isn't a big problem */
+				if (BaseMedia<Tbase_set>::used_set == duplicate) BaseMedia<Tbase_set>::used_set = set;
+
 				DEBUG(grf, 1, "Removing %s (%i) as base " SET_TYPE " set (duplicate)", duplicate->name, duplicate->version);
 				delete duplicate;
 				ret = true;