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The code which removes the files after being uploaded is only in one place; it's not something we add in each post-processing engine. As long as all of your files have been successfully and fully uploaded, the originals are removed from your web server.

What you are saying here tells me that the files probably didn't make it to the FTP server. Remember that FTP does not allow for splitting uploads into multiple chunks, therefore this may be relevant: 

Most failed uploads are caused by timeouts. PHP and your web server have time limits, i.e. the maximum time a PHP script may process data before the web server aborts it. Uploading the backup archives to cloud storage takes time, the exact amount of which depends on the size of the file and the network speed. If that time is over either time limit your backup will fail. The time limit and the bandwidth are beyond our control. The only thing you can control is the size. Many post-processing engines support chunked uploading (breaking up the uploads in smaller bits and having the remote server piece together the file) and you can change their chunk size. A chunk size of 5 or 10 MB works best in most cases. For those post-processing engines which don't have an option for chunked uploads you will have to change the Part size for split archives in the Archiver Engine options. Again, a value of 5 or 10 MB works best in most cases. This setting will split our backup archive into multiple files (same base filename, the extensions are .j01, .j02, ..., .jpa; or .j01, .j02, ..., .jps; or .z01, .z02, ..., .zip;), the maximum size of each one being the value of this setting. To restore these backups just place ALL of these files in the same directory and choose the main .jpa, .jps or .zip file: the other parts are discovered and extracted automatically.

I don't have your log file, but what I suspect happens is that part of the backup archive gets uploaded before you hit a timeout. Since the backup is complete it appears as OK (completed) in the Manage Backups page, but since the archive did not get fully uploaded to the FTP server you don't get the only full copy of it which is on your web server removed either. Changing the part size to a lower setting would help with that. Depending on the web server and FTP server I have seen sites which need something as low as 5MB and sites which can go as high as 250MB for the part size. I have yet to see a site which can go all the way up to 2GB or more, unless both servers are on the same local Gigabit or better network and there's no other traffic restricting the throughput.

You're welcome!