yeah there's a file called something like game.toc which specifies the filenames, offsets and filesizes of all the files in the iso. .toc is a well documented format you can easily find the spec online but if not I can explain it to you. It would be trivial to write some code to manipulate the filesizes. I think as long as the .toc file matches it should be fine.
Yeah articuno has some icy sparkles around it.
From what I saw inspecting the binary data by eye the two formats are very different. If you look at bulbasaur from X D and bulbasaur from PBR the data doesn't share any similarities as far as I could tell. Importing them to Colo/XD would be a case of converting from one format to the other.
Someone made a program that converts PBR models to .obj a while back. I managed to track down the code. I could send it to you if you're interested.
Sorry man, not sure how to help with that. You must have accidentally ticked something illegal in the save editor. You could maybe try catching a wild pokemon and using the editor to change it's stats in order to recreate the ludicolo?