Duplicate files · Choosing which copy to keep
How do I keep a different copy than the one recommended?
Short answer: Click the round selector beside the copy you want to keep. The selected copy stays and the rest of that set are what the set's remove button takes away. Clean all uses the recommended copy for every set, so clean sets you've changed individually.
In each set, click the round selector next to the copy you want to keep. The selected copy is the one that stays; every other copy in that set is what Move … to Recycle Vault will remove.
Your choice applies to that set only. If you then use Clean all — keep the best of each, it uses the recommended copy for every set, so for sets where you've chosen differently, clean them one by one with the set's own button instead.