Reproduction steps:
1) Open users' attached project
2) Make sure "Scene1" is loaded
3) Play scene.
4) Press "Space" button (it has to load "Scene2" additive)
5) Press "Space" button again (it has to merge both scenes)

Expected result:
Both scenes are merged and GI stays same as for 2 separate scenes.

Actual result:
After merging scenes GI is corrupted for "Scene2" objects.

Reproduced with:
5.3.1f1, 5.3.2f1, 5.3.3p3, 5.4.0b10.