If you are upgrading Sitecore, after you have performed all upgrade steps delete the indexes folder and rebuild all indexes.
I have experienced issues recently with some unusual indexing problems. Indexes would become corrupt and unusable only to be fine after a rebuild and then break again hours or days later. Some trawling of the internet lead me to a post suggesting to delete the indexes completely rather than just rebuilding. Although the indexes I have took best part of 24 hours to rebuild I followed the advice and hey presto it is all working again, although with several days lost.
I suggest you do this regardless of any issues to save you the time later when it rears its head unexpectedly.
Ben Richardson 