I do not know if someone can upload just these files by themselves for violation of terms or stuff, but I would think that even though it is a hassle, you should just uninstall and reinstall TDD. If you don't want to do this, you MAY be able to get away with deleting all the files which have a later date modified time, but I wouldn't recommend this, because it could in turn just result in a reinstall anyways.
Where did you purchase your game? If you got it from Steam, just uninstall and redownload the game, then re-import the AAMFP assets (if needed).
If you do not have Steam and bought a retail copy, you can redownload it from here:
https://shelf.frictionalgames.com/