Other info: my themes and settings survived and were still there after server reconfiguration. All in all, pretty easy to get everything back up as before.
That's really strange. I've never seen this happen before, and I can't think of a way it could happen. I don't think it’s related to iCloud sync, since server configurations are actually the one thing that isn't synced (syncing them would cause all sorts of issues 😅). The downloaded books disappearing is even stranger, since those are stored as files by the system and aren't affected by iCloud sync either. Thanks for reporting it though. I'll keep an eye out in case anyone else runs into something similar.
I found a rare bug that could end up deleting the stored credentials when certain errors occurred. That should be fixed now.
Just to add, I had an issue where my server config would be lost almost every other day. To be safe, I fully uninstalled the app and reinstalled with fresh config. It hasn't been lost since.