http://bugs.winehq.org/show_bug.cgi?id=9959
--- Comment #3 from Austin English austinenglish@gmail.com 2008-01-01 21:27:58 --- I was thinking about this earlier and was getting ready to file a bug for it but found this one.
How about a little file in .wine or a registry key that is read upon running wine, and should match the current wine version. If it doesn't, call wineprefixcreate (or pop up an error saying that the registry is outdated), which then updates that key to the current wine version. Shouldn't be too much overhead and prevents quite a few problems.