So, I deleted all duplicates (ca. 10.000 of 40.000 files) in the Backup folder and only kept the originals.
What happened next is that the iPhone My Cloud app tried to sync ALL files from iPhone to the Backup folder, creating duplicates again. This makes no sense - why does it not recognize that the files already exist in Backup? Of course, I checked whether the duplicates already exist on the iPhone but this is definitely not the case.