I think we're all trying to hit the basics first, so let me take a stab - have you tried a third party indexing tool to search for a string inside the files (including 'invisible files')? Just trying to eliminate the variable of the files existing, but not being indexed or shown due to a corruption. Afraid I'm unfamiliar with the best third party search tools on Windows, but there must be something similar to DEVON EasyFind on OS X.