No, because any files that have never changed still have their data in the original upload files.
EDIT 1:
If you did this after it ran a compact, the compact might already have decided to delete the file.
“listed as Deleting” is (I think) meaning it tried a delete that failed, so it’s going to try that again.
This sort of situation might also be possible in some error situations, e.g. an upload error gets retried under a new name, and the old file (whose integrity is unknown) might then be deleted.
If a maintenance window is possible (hoping no attacker slips in), that might be one solution…
EDIT 2:
New currently not-quite-Beta Duplicati versions have more secure ways to store the credentials.
I haven’t used it yet, and it’s probably not as solid as chattr, but chattr is sometimes too solid…