When Atlas Size of lightmaps are set to 4096 under Baked GI tab, Unity generates 4K maps and stores the information but by default, imports the lightmap as a 2K map. The workaround is to manually set the max size of all lightmaps to 4096 under import settings in inspector. When the user bakes the scene again, same steps should be followed.

Steps for reproduction:
1) Open the scene "4KTest"
2) In Lighting > Baked GI tab, choose "4096" as Atlas Size
3) Build the lighting
4) In Project tab, find the "4KTest" lighting data asset folder.
5) Choose the lightmaps and in inspector, observe that "Max Size" of lightmaps are set to 2048.

Notes:
- Tested in 5.4, 5.5 and 5.6.0a1