Apple Loops Are Gone, But Still In Folder

All my apple loops have disappeared from Logic Pro, as well as a lot of plugin presets.
However they're still in the "/Library/Audio/Apple Loops/Apple/" folder in the following folders
Apple Loops For Soundtrack Pro
iLife Sound Effects
Jam Pack 1
Jam Pack Remix Tools
However Re-indexing the loops inside of Logic doesn't re-index them and can't find any loops.
Any suggestions? Would there be like a cache file I have to delete or something?
This happened around the time of the 9.1 update

Maybe your Spotlight index is corrupt or disabled for the drive where the files are? People have ben running to this problem when disabling Spotlight. Try reindex using a program called OnyX. Maybe there is other ways to do this.

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