It might be super early for me to actually think as that seems a little wonky to implement something that would be logically a bit confusing.
Wouldn't it be easier to just make two folders on the remote and store all your data in remote:data and sync remote:data and have a backup folder with remote:backup? I might need more caffeine though.
I am trying to avoid something like that since it breaks with everything else I am doing. But that’s my problem.
Since I have the list of files I can just do an rclone moveto with flags to try to speed it up. Certainly less efficient but not the end of the world.
One idea though if this was something worth doing is to make it so that while they can overlap, you can’t backup into the backup. So a backup-dir flag is also an implicit filter. In some ways that makes more sense! Just a thought.