This is a duplicate of earlier issues marked as resolved, as it is clearly not resolved.

How did it happen?

Multiple mobs (animals like Horses, chicken, wolves, pigs, sheep) were fenced in away from chunk borders.

Travel 200 blocks from mobs location (farm) to a Zombie Dungeon,

Cleaned out and rebuild / modified the dungeon for the purpose of zombie harvesting,

This took about 60 minutes.

Saved the game at the zombie dungeon location 200 blocks away from the mobs location

Exited the game to desktop.

(Re-) Loaded the game directly with the made shortcut on the desktop.

Travel back to the farm (mobs location) over half of all mobs were gone (2 from 4 horses, 1 saddled horse, all sheep, 20 out of 50 chicken, 4 of 9 tamed wolves, half of all pigs, 10 of 25 bees).