Downloads files are deleted immediately after the main file records are *permanently* deleted (not soft deleted). There are occasions where "unclaimed" files may remain however. For example, if you upload a file on the submission form and delete it or upload without submitting the form then these will be retained in case the user returns to submit later.
Those temporary files are deleted via a task after one day so if your tasks weren't running or you took your backup during that 1 day period then it would explain why you may have had some redundant files.
I hope that helps.