Since one of the latest Virtualmin updates multi-destination backup no longer works correctly.
If destination 1 is a local folder and destination 2 is an FTP, backup will be made on destination 1, transfered to the FTP then deleted from destination 1. The backup log will succeed without indicating this behavior. That is, backup on destination 1 was deleted.
The bug was probably introduced in 3.95gpl or 3.96gpl
In my case this was a scary discovery. My long term backup is on destination 1(NAS) and my alternative "fail safe" one day backup on a FTP. Please fix this critical bug asap.