I happened to have a video say "this-is-a-video.flv.php" and I uploaded a MP4 version of the same thing such that its page was "this-is-a-video.mp4.php". Anyway, when I deleted the FLV version, it deleted the MP4 one as well. Now, I am sure the reason it did so was the filenames were the same except for .FLV and .MP4.
It probably shouldn't really do this?
Anyway, I re-uploaded the MP4 version and left the FLV off. Next time I'll use a different filename so it doesn't happen again.