How do I remove a prefab from a subscene? What does it even mean?

I am running on Unity 2019.1.1f1
I previously had a GameObjectEntity component on a prefab, and it would give a error stating it being in a subscene and therefore auto converting to entity and couldn't do it because it had a GameObjectEntity and then it would re-import it forever
Now I managed to remove the GameObjectEntity without breaking everything, but it still re-imports the prefab forever so long it is selected in the editor, I can only assume it's something to do with the subscene thing, as the issue started with it.
I've even tried deleting the prefab and recreating it from the scene window

This is what is happening when I select the asset, and it only happens with this specific one

I assume this is somehow related to the DOTS because it started happening when I updated the DOTS package, This was quite a long white ago and I assumed it would go away when I managed to remove GameObjectEntity from the prefab. This started happening on the same update that deprecated GameObjectEntity

All my DOTS packages are up to date