I had this happen with some warnings as well where it wouldn’t just go away. At that point I removed the whole UnrealEngine hidden folder under: current user → AppData → Local → UnrealEngine. I kept the other folders there for the header and launcher.
Now this will cause the engine to start like the first time again but it removed and corrected any warnings like this for myself. It’s by no means conventional but it solved my warnings about missing assets that were long gone and removed. I figured where is the other cache being stored for this stuff and that was my answer.
Hope this helps.