Just or awareness this is happening on PMS v1.25.0.5246 on FreeBSD as well. I can’t offer a lot to help with this because I only recently started using collections for Christmas movies so I don’t have any history to judge it on. I also upgraded my libraries when offered.
That said, the three collections I have made are losing movies pretty consistently. I have tried a few of the actions discussed (re-scan all, rebooted the server, added some collection tags manually, added some via ‘add to’, and locking the collections tag field on some of them). I will see how it goes and report back any interesting findings.
personally, I’ve never enabled the ‘Empty trash automatically after every scan’ function;
I’ve never enabled the ‘automatically create collections’ function.
As I said, I think that a solution could be that, adding a movie to a Collection via the (in)famous vertical-or-horizontal-three-dots-menus etc., the software takes automatically care of locking the relative padlock (substantially, no difference from when you manually insert the Collection name from the Editing page.