How do I clean up my Libronix book Files?

An excellent question with a two part answer.
You especially need this tip if you've just used PBBMover or PBB Updater.

Libronix keeps it's "book" records in an internal database so if you move or delete a file you should tell Libronix to rebuild it's cache, then we'll get rid of some duplicates through a special Libronix report built just for that purpose.
Rebuild Your Cache
First navigate to Tools > Options > General...

In the resulting dialog, click the resources button, check that your paths are correct and click "Refresh Resources".

You probably should close and restart Libronix twice and give it plenty of time to sort through and re-recognize all of your resources.

Remove Duplicate Resources
Second you'll want to consider removing some duplicate resources.

Navigate to Tools > Library Management > Remove Duplicate Resources

Select the books to remove

these will be removed from both the database as well as your hard drive so make sure!

Notice the three types of boxes in the image. The grayed out box means that it's in the database but not on your hard drive. This is a clue that you need to refresh your resources as above. The other two boxes show resources on your hard drive and the check indicates the one that will be deleted.