HEU_Asset updating prefab with single output will result in missing mesh when placed in scene, but when opening the prefab, the mesh reference will still be there.
The missing mesh isn't seen as an override on the prefab in scene either.
Only when removing the mesh from the prefab (set to none/null) will the prefab rebuild/update properly.
This only happens when the build prefab has no child objects (and the mesh output is on the root of the prefab)