There's no real way to tell in advance if you are going to take a hit during the downloading, or 2 mismatched files are being merged, but you can check to see if others have had problems with that particular file.

Try a Bitzi web lookup first. And contribute to the effort - it's open source. Download the bitcollider software and and report on the files you download, good or bad. And no, I'm not affiliated with them in any way, I just happen to think it's a useful system.