Safepots uses an incremental backup method. After the initial full backup, Safepots will start acting in an incremental mode, in which only the new and modified files will be backed up, saving your bandwidth and creating file versions on the server side to allow you to go back to an older state of the file when needed.
The file(s) which you will be deleted from your source drive(s), will not be deleted from the backup. For more information, please check this article.
The same applies to Safepots.