I’ve fixed this in a mod if you are able to install mods. It is “Fixed Wells…” on workshop.
For devs fixing, there are two problems. One is the HasBeenPlacedInWorld bool is sometimes lost after a restart, and the other is doing a take all for an inventory with stacked items will leave behind null items. A basic hive will check if there are 5 items in the inventory and stop if so. After a take-all there will be 5 null items.
Often it will make one more honey and then stop. This is because the item removed event doesn’t check capacity. So if you can’t use mods you might try putting items in and out to get it going again.