It is the only issue I have with projucer, since I started using it. I have no problem adding modules, creating or deleting files.
I do not understand what is happening, so I cannot give specific details. I just know that everything is out of sync. When I think I have fixed it in Visual, in projucer it returns to the previous file marked in red.
It is not serious, I always manage to fix it by removing the old references and adding them again, it is just a nuisance.