You'll need a a tool that can rebuild the cpk, then you can rename that cpk to Data1.DNS and replace the iso's original file. Apparently it's not necessary to reencrypt it to PGD?
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There are some programs like CriPackedFileMaker and CPKTools that can build a cpk given a directory of files, but when I tried these out the result wouldn't load in ppsspp. I'm not sure if that's because the quickbms script is unpacking the cpk improperly, thus preventing a proper rebuild, or if the rebuilt cpk is not compatible with the game's original cpk version CPKMC2.18.04, DLL2.78.04