Try searching your hdd for the files. From your desktop go to Start>Search>All files and folders, and search for a file name. Then you can add the folders back into limewire, Tools>options.
If you can't find them, then possibly they have been deleted. You will need a file recovery program to get them back. See this thread for more info:
DELETING FILES FROM LIMEWIRE LIBRARY-DON"T! - File recovery advice!
This thread might help also:
If You Stopped Sharing & Now Cannot Find Your Shared Folder, READ THIS !