Report: I was able to fix it. But the solution isn't pretty.
I think it has something to do with when I imported the models, I didn't immediately make sure that everything is local to scene, and so when I removed the scene that contained the original MeshInstances, it didn't save it as local to scene, even if I had it on.
In the end, I have an older version of the project, reimported the models, with local to scene turned on in the first place and not deleting said scene. I set it up the same and it ended up working as it should.
This isn't exactly the solution I hoped, and if this is something to look into for the devs then please do.
If you're in this situation, I would advise you to reimport and local to scene all meshes at the very beginning. I spent around 4+ hours on trying to figure it out and in the end, just restarting and being aware of the problem just became faster.