I have done everything that has been suggested. I have rebooted/restarted the server multiple times. Manually scanned each library as well as scanned all libraries multiple times. I have verified that the collection directories/files still exist. I have refreshed metadata. Nothing works. They do not return. They don't appear under the collections tab, but all of my movie collections are fine. I suspect because these are done by autoboxset. I also re-installed the server. Nothing has worked.