Funny this came up. I had a similar problem last night and have been able to duplicate it in the past. For instance, I handbraked a movie using AppleTV preset and took the resultant file and fed it through to MetaX. I tagged it and dropped it into iTunes. A few months later I noticed I had tagged it with the wrong genre.
So I right-clicked "Get Info", changed the genre, and clicked OK. iTunes says writing tag, and just sits there forever. I finally forced-quit iTunes, relaunched, but now the video, while still showing the proper size, bit-rate, and FPS in movie inspector, has no video or audio. It's annoying to say the least. Anyone have any ideas?
And I did try squeegify, but no luck. And this is on a mac.