Chicken jockeys spawned with no nearby chickens can have the chicken despawn, which is normal. However, when a baby zombie mounts an existing chicken, the chicken gains the ability to despawn, causing the existing chicken population to slowly decay if left untouched. This is probably caused by the IsChickenJockey tag being activated for existing chickens when zombies mount them, which doesn't need to happen, because zombies can still control chickens without the IsChickenJockey tag.

How to replicate:
1. create a new world in creative (super flat is best)
2. Spawn in a regular chicken
3. Spawn a ton of zombies (command blocks with a fast redstone clock is best) until a baby mounts the chicken
4. Get rid of all the zombies
5. Teleport 128 blocks away from the chicken
6. the pre-existing chicken will have despawned