Not going to claim I’m good at c++ with unreal yet.
But from what I can tell, I would call this a bug with subsystems.
I tried to store a reference to both the objects that I’m storing in my subsystem from before, in my GameInstance Blueprint as well. And now the data can be accessed from the subsystem without issues!
So for some reason, after a level gets changed, I claim that garbage collection misstakenly delete objects that are only stored in the subsystem. I will have to do some more research before I report this to figure out if this is in reguards to any type of object or just blueprint objects etc.