First, make sure if you "List All" from the admin, you really do have links the database.
If the links are gone, several things could have happened.
Try re-indexing and rebuilding the site.
I've also had links disappear after making "minor" changes to the sort orders in the files, so if you made any changes to the code, back out of it.... It might make sense to you, but for some reason it prevents links from being added to the link output hash.
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