In 4.6, if you rename your custom GameInstance blueprint, editor will quietly allow you to have a null GameInstance. If you try to play game, you get a nice crash:
Assertion failed: Class [File:D:\BuildFarm\buildmachine_++depot+UE4-Releases+4.6\Engine\Source\Runtime\CoreUObject\Public\UObject\Class.h] [Line: 2532]
ConstructObject called with a NULL class object
Expected behavior should be that configuration file is updated with new GameInstance blueprint’s name.