Viewport invisible and NavMesh breaks after "building all Levels"

Every time I rebuild all levels, most things in the Viewport get invisible and the NavMesh volume stops working. Started happening after I deleted lights from the scene which UE5 flagged as performance heavy (Reason given: some lights overlapped with more than three other lights).
When I load into another Level and load the original Level afterwards, aswell as deleting the old and broken NavMesh volume, everything starts working again.
Another unique thing that sometimes happens is, that when I want to use the “save all” or I want to close the Engine, I get asked where I want to save the Level, like I just created a new level file. But I have no idea which level is supposed to be saved. If I save the “ghost level” under a random name and open it, its a copy of the exact same Level as I was using before. The original Level still breaks though.
And yes I have everything enabled in the “Show” tab in the editor.
And also disabled the cinematic Viewport with no result.

The aborted messages come from a print string that prints the “movement result” of AI move to.