Sometimes files and folders that shouldn't be deleted are found in the thrash

[Kimboz]

I am finding increasingly often files and folders that shouldn't be deleted in the thrash.
It feels like FFS (A program that I routinely support by donating) can't really guess whether a file must be deleted in the folder where it's present or should be added to the folder where it's missing.

I use the program mostly to keep a backup HDD updated with the content I progressively add, but sometimes the HDD is the folder where the new content is first, and them my main HDD need to be updated.

I hardly ever need to delete anything (that is: when stuff is moved/reorganized from a folder to another) and then (and only then) deleting for the sake of moving) should be an option.

I feel like I'm not getting this right in my settings. Could you help me please?
Andrea