I got this when converting a project from 4.8 to 4.9 and I think I found the source of the problem.
At the same time, I was looking up how to properly rename projects. I noticed that using the proper ‘Create a Copy’ method for making a new, updated version of an old project places everything in a folder with the same name expect for an appended version number. However, the config and project name entries were left as they were. By renaming the old project and making sure that the folder name matches the project file name, all the warnings stopped appearing.