I can confirm, the intended behaviour is for the files to be hard-linked from /Downloading to /Downloaded. You can do whatever you want with the files in /Downloaded (rename, move it, delete it, whatever), and seeding can continue with the files in /Downloading . Once seeding is complete, it auto-deletes the files in /Downloading. The files in /Downloaded should stay where they are until you do something with them.
@txhermit If the behaviour is something else, it's indeed not normal, but also quite surprising since I've been using the app quite a lot without noticing any problems. Do you have any kind of custom configuration or something ?