To fix this issue, you must tell Unreal to load up these assets explicitly, otherwise, it doesn’t know to use them. I had done this before and completely forgot somehow!
To do this, go to your Project Settings->Game->Asset Manager and you will find the “Primary Asset Types To Scan.” You need to add an entry for your blueprint GameInstanceSubsystem. To do this, select the class type and set the Primary Asset Type to the exact name of the asset. Also make sure to set the Directory to search for the asset. Also, make sure to tick the box saying “Has Blueprint Classes” so it knows that it’s a blueprint.