Can you reproduce this or is this just randomly resetting some things? Do you have any players that are connected to that library that run all the time? I had a problem once with playlists getting overwritten randomly and the songs I just added disappearing. Turned out that another client that I had always running overwrote the changes I made.
Thanks Max - I'll do some more digging and see if I can reproduce the issue, including in circumstances other than I've outlined below. Yes, I have two raspberrypis running continuously with similar settings. There's also four other J River clients running on the network - two windows and two mac - so it could be some other odd syncing issue as well.