If you are messing around with the inards of xcf files you might want to try the Pronto Script Support tool at my web site (
www.the-gordons.net) It takes an xcf and breaks it down into its parts and builds a GUI over the scripts in the file.
Invoking a script will open whatever editor assigned to the extension js. It holds all of the material including the collection xml in a working directory.
It rebuilds the zip file at any time (Save) and will also invoke PEP to allow a rebuild and download in a smooth operation. It knows about the comment object and handles it properly. It works just as well with xcf's for the 9400 AFAIK.
I never use the PEP editor to edit Prontoscript. I use a full screen syntax checking editor that displays syntax in color and spots 90% of my errors before I load the xcf into the Pronto.
I only use PEP for laying out screens, and then I only use the 9600 one if if I am building for the 9400. All that extra real estate in the 9600 allows for interesting capabilities when the target is the 9400.