you only need to replace game.rxproj with the same file from your current version, it wont delete any of your progress in your project, all that is stored inside the data files, also i remember a small bug that occurred when adding and removing extensions with the gui tool, if I remember correctly when you delete an entry it does not fully remove it, it just leaves a blank named extension, open up the config file thingy and check the extension part to make sure that is not the case