I had the same problem, but found yet another solution.
Let me state my problem so that we’re sure we’re talking about the same thing.
I had a file in a directory where a bunch of code files were and some of the files in that directory were shown as “in my project” and some of the files were missing. I wanted the missing files to appear in my project.
I simply selected the folder in my project and pressed ‘F5’ or right-clicked and selected ‘refresh’ and the files appeared in my project. It looks like that is the intended way of doing this.