Deleting a tilemap in a grid prefab and saving back that prefab creates a duplicate in scene

Repro:
1- Open scene 'Tilemap'.
2- In scene hierarchy, select gameobject 'grass/Tilemap'.
3- Delete gameobject. You'll get a prompt saying you're breaking prefab, continue.
4- Press Apply in inspector to update prefab with new values.

You'll notice the prefab has now been duplicated in the scene hierarchy. If you look in Tile Palette, you'll also notice there are still to tilemaps in palette, but both are named 'level_02_background'

Reproducible: 2017.2.0b9, 2017.3.0a5 (e36fc2cf0775)