Recently, there has been ongoing issue wherein a player's villager hall got wiped out ( specifically enchants that are essential). As far as I know, it was still under investigation, but when I logged in the next day. I have experienced the same issue : "My villagers are missing".
I lost three villagers.... Two essential ones and the other one that I can just forgive bout happening. I have no clue how it happened since I wasn't around.
The possibilities I could think of are entities spawning inside the hall (event spawns?) and killing the villagers. Another is entity-culling which has been a known issue from other villager breeders ( I think there is a certain limit of entities within the chunk as far as I know). Lastly, player instigated murders which is considered and punishable for griefing.
Because of these possibilities and the known fact that these villagers aren't recoverable by any means, wouldn't it be better to bring back the player's authority to adjust flags ? Specifically, enter-claims to avoid unwanted players or entities inside the claim and entity-spawn/entity-damage flags to disable event spawns in the area or if that's not possible then at least make the hostile entities unable to damage villagers with entity-damage set to false.
I think this should be reconsidered issue as the best course of action right now is just investigating the culprit which doesn't solve the issue of prevention from happening.