I found this forum post and will revive it appropriately just in case anyone is still lurking at this topic. I found the solution and for me, I was working with Visual Studio Code and it turns out running the WRONG build task will cause this problem.
I originally ran the “Win64 Development Build” and then this error happened when I re-opened my Unreal Project. The task I was SUPPOSED to run was the “Editor Win64 Development Build”. After I ran that on my Visual Studio Code and then opened up my Unreal Project, everything that was missing from the map was restored.