Workspace file disappears on saving changes Projucer

Everytime I add a file in the projucer and hit save while Xcode is open I get the following:

The workspace file that was at “PATH/project.xcworkspace” has disappeared. Do you want to re-save the container, or close it?

Closing it is very annoying, because I have to reopen it obviously but also the file tree on the left is reset etc. Re-saving seems to do what I want i.e. just let me continue to work, but I’m not sure wheter I am undoing stuff Projucer just did in that case.

Either way it’s a bit annoying.

Secondly what I don’t like about the Projucers is when a file is selected so that on the right there is the editor and I hit command + S the file is saved, and not the project. I never want this, and it has bitten me in the ass a lot off times where I thought I had saved/updated the project but I didn’t.