Alright so I've looked around the forum and there seems to be alot of info about how to recover deleted files.

Here's my problem, I didn't delete them. I downloaded the latest upgrade for it and it was all going well until I looked at my library and its empty.

So, are they still considered "deleted" and require a file recovery program? Or are they just missing and I'm crazy?? Thanks for any help.

They aren't deleted. Limewire just lost the connection with them. Just search your computer for a file you know was in there and then add the folder you find to limewire library.