When I returned to the village after digging for ore, more than 20 villagers and all the animals (chickens, cows, etc.) that they raised were gone, leaving only their home.

It could be because of they despawned?

@Bill Passive mobs don't despawn

Please check your game logs (.minecraft/logs) for death messages.

I opened all the logs for that day and searched for "was slain by". But it just says that there are no search results. In this case, is it a despawn rather than a death?

i think in the case of the animals it was just a despawn because you went more than 128 blocks away

@phonia animals don't despawn. Otherwise animal farming wouldn't be viable. 

Come to think of it, there was a harbinger of the events mentioned above. I slept with my tamed cat, woke up, sat it down, made a deal with the locals, and when I returned home, the cat was gone.

May I ask if this world was ever touched by mods of any kind? Some third-party modifications have been known and responsible for making entities supposedly disappear. If you didn't and haven't used any mods before on this world, could you please provide the world file so that this problem can be further investigated? Thanks in advance.

_{This issue is being temporarily closed as Awaiting Response. Once the requested information has been delivered, the report will be reopened automatically.}

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