Repro steps:
1) Open my attached project and BakedPrefabs -> BakeLightmapPrefabs.scene
2) Click on Tower object and scroll in the Inspector to see Prefab Instance Data component
3) Notice that there are Lightmaps dropdown, make sure it's size is 1
4) In the Menu bar click Assets -> Bake Prefab Lightmaps
5) Click on Tower again and notice that Element 0 is empty (see .gifs)

Expected: Texture2D lightmap is assigned to the object's Lightmaps
Reproduced in: 5.4.0b3; 5.3.2p1
No repro in: 5.2.3p3