I'm not entirely sure how the swarm feature chooses and creates final files from multiple sources.

From my experience, if one source gives corrupted data, then a final (swarmed) file that used part of the bad source, also is corrupt, and must be deleted, and a new download started. In this case, my suggestion for a cleanup button, would just facilitate a quick easy way to perform the delete (with all other unneeded files as mentioned above).

However, if you have two files that downloaded independently with similar names... i wouldn't have expected the cleanup button to affect those at all. For one, they would not be prefaced with the word CORRUPT- or PREVIEW- so would be left alone to continue to download from its (hopefully uncorrupted) source.

Therefore, the cleanup button would not harm other downloads you might have.

(I hope i didn't miss the purpose of your question.)