- Patch #938560 by Damien Tournoud: fixed {system} records of installed modules are removed.

modules/system/system.module

@@ -2184,9 +2184,11 @@ function system_update_files_database(&$files, $type) {
   }
 
   if (count($delete) > 0) {
-    // Delete all missing files from the system table
+    // Delete all missing files from the system table, but only if the plugin
+    // has never been installed.
     db_delete('system')
       ->condition($delete)
+      ->condition('schema_version', -1)
       ->execute();
   }