Hi just got around to testing this, and it looks like a bug that only happens when you delete a layer underneath a layer that contains prefabs. So if you have
A
B (contains prefabs)
C
and you delete A, you're fine. If you delete C, the prefabs on B lose their contents. You can work around this by moving C up so its at the top of the tilemap stack and delete it. I'll fix it properly in the next version