Your problem is related to this other question: Setting an icon to kicad files
What’s probably happening is that .kicad_pro is mapped to the mime type text/plain and various applications like text editors have been registered to handle this mime type. When you edited the rule you were editing for all objects of mime type text/plain.
What has to happen is that .kicad_pro has to map to a different mime type, I think applicaion/kicad, and kicad has to be registered to handle files of this mime type. As to how this is done, I’ve never looked into it since I use the KiCad interface or the command line interface, rather than the “object oriented” desktop interface. Sorry I can’t help further.