Same thing happened to me today while playing local co-op, here are some of the weird things I noticed the day before the animals disappear:
- Every animal I petted the day before disappeared, including pet cat.
- There were animal duplicates, the ones that came outside looked normal, the ones inside were like "clones" and you could interact with them (collect milk from this "duplicates") and when petted, only the arrow from the conversation bubble was visible
- Also lost a preserve jar that I placed inside the 2nd player house, when placed, it started jittering like when you interact to remove it, and when I did removed it with the pickaxe, it just did the pop animation, but no item in the house, tried the same with other items that were already placed but I couldn't interact with it
- I slept in the main house before this day, but woke up in the second bed in the second house (the 2nd player house had 2 beds)
If it helps, it was the day before an community center bundle unlock (aquarium)
It happened on the 6th of Sprint, 2nd Year