This is not a problem instead it is a very helpful feature in FusionRetail6. FusionRetail6 forcefully set ‘Method of Communication = Offline’ whenever you take a backup as a precaution measure to save your data from unwanted modifications.
FTP is an online file transfer protocol. It uses internet connection and automatically transfers data to the remote server. So after restoring if you alter or modify any data it can change the data of working database (in HO and Branch).