I also used to back up other PCs to each other somewhat regularly, and sometimes I'd end up with those files back on the original PC in a backup of another. Fortunately, when I switched to borgbackup on Windows as well [1], this massive reduplication of files became a solved problem.
[1] borgbackup doesn't officially work on Windows, but I run it in WSL which does reasonably well for all the files I really care about (i.e. the stuff I've made). When they have particular unusual characters in the filenames, it throws up a warning for that file every time, but otherwise seems fine. I've never bothered investigating whether those particular files restore to the correct filename, because I know I've also backed up the zip file those files have come from and it's just accidental that I've backed up the extracted files as well.