Incremental backup - not deleting files (and not finding a way to do it)

Hi everyone,
I need to migrate some domains from a Virtualmin installation to another, in a different data center. Some of them are quite big (20 GB), so backing up and restoring takes a long time and, meanwhile, traffic happens (mails arriving, being read, deleted, databases modified, files uploaded and deleted, etc).
I’ve tried the “incremental” backup option and it speeds up things a lot (they’re mostly (busy) e-mail domains), but there’s a problem: files are only added, not deleted. So if people read mail and delete them between the full and incremental backup, they will find them again after the incremental restore. Same for files.
Am I wrong? Is there a way to say “hey, it’s incremental, so delete what’s not present anymore”. I’ve found an option in the restore tab, but doesn’t seem to be working.
Thank you