Problem: After reindexing to update my "User Loops" Logic completely removed the stock Apple Loops index and would not let me reindex them. (Even after deleting all Mac HD and User index files and folders)
Solution: Use garageband to reindex loops and it will also reindex them in Logic.
Certified Logic Pro 9 Trainer
Logic Pro 9.1.8 Mac OSX 10.8.3 Apogee Ensemble & Duet