A few days after taking a snapshot of my Seafile server and then upgrading, I was alerted by some users that their libraries were missing. My first reaction to was restore the snapshot as another server and fetch libraries from there. Unfortunately, that appeared to have the same issues, indicating that it was not an issue with the upgrade. Luckily, Seafile has a repair tool that I recommend using in such cases, and is probably a good idea to run every now and then.
Simply go into seafile-server-latest folder and execute:
It is a good idea to stop the seafile processes first before running the check, and then restarting them when the check has finished. You may not see your libraries re-appear if you leave the seafile server processes running whilst the check is being performed.