I was breeding my cow farm and when the new snapshot came and the server got updated. The cows were gone. Same thing happend to villagers i had, chickens, dogs, etc

The server upgraded from what version to what version?

It was from 15w31c to 15w32a

Ya, same thing happened to me, it seems that passive mobs despawn when the certain chunk is unloaded.
I had dropped off some newly tamed wolves at home, go out at night to get exp, and returned home to find wolves gone.
Current Version: 15w32b

The duplicate issue that was attached to this seems to be different from mine. I had a villager in a minecart and it disappeared as well.