This isn't a very good fix and probably won't work for everyone. But I found if you save your lot to the gallery and start a new world the stuff on the desk under a bunkbed won't disappear anymore. I have also tried (while writing this) that if you save the lot after adding the bunkbed and desk then bulldoze it then finally replace it this also gets rid of the disappearing desk items. However, This does also mean everytime you add a new bunked and desk you will have to go through that process again.
Hope this helps someone else who has also been having trouble with this 🙂
