Entities riding something do not store this when the chunk is unloaded and dismount when reloaded.

If an entity is riding a minecart or skeleton upon chunk unload, it will not store this in an NBT tag and will separate when the chunk is reloaded. A possible fix for this could be to assign a NBT tag that defines the persistent entity ID of another entity to continue riding. This also includes the player riding a minecart, saving and quiting and returning to be out of the minecart.