Hello ,
Usually when the Externally Referenced warnings pop up after upgrading to a new engine version, it’s due to the engine content / starter content / template assets, etc. These are included with the engine itself so it may be trying to reference ones from the previous version of the engine. If you’re using any of these, try migrating the assets from the new version that you’re using. If all else fails, you can also try migrating your own assets into a brand new project in the new engine version and see if the problem persists.
Hope this helps!