We strongly recommend using a Muse admin console to do an Application backup instead of creating a copy of the Application's directory.
The backup/restore feature is available starting Muse 2.2.0.0 and was especially created for such purposes. It backs up an entire Application under the "${MUSE_HOME}/admin/tmp/backup/" directory by creating a file with the name "${APPLICATION_ID}.${timeStamp}.bak" for each backup action.
Multiple Applications can be backed up simultaneously - however, the restore is a "one Application at a time" process. Also, a single Application can be backed up multiple times; upon restore, the user is prompted with all the backups ever made for that Application.