Yeah, I decrypt and crunched the update-only and applied it to bas's existing compressed version of 96.... Everything worked well aside from System.json file. (Why it did not work and why the game couldn't find IconSet.png in img/system - I don't know, because as said it works with the encrypt files .

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Correct, applying the update-only files on the uncompressed version worked w/o any error for me too.
Ok, this answers my question. You you applied the update-only on the uncompressed version and crunched it then.
Thanks for replying to my question.