Here’s one thing I noticed (which is probably an unintended bug) a while ago that might be the cause.
If you use the overflow menu to add items to a collection (… > Add to > Collection), then the collection field does not get locked. You can check by editing the item after and see that the lock on the collection field is not orange. With this knowledge, it is possible that a future metadata refresh, either manually or with the “Refresh metadata periodically”, erases the field since it isn’t locked. This is my guess but I haven’t verified it yet.
Side note, the collection field does get automatically locked if you edit the field directly from the edit window. So this method should keep the collection locked after a metadata refresh.
