I would like to have the CIA as closer as a legit one. None of my converted CIA are region free, all EU. And as riku said, the program re-encrypt everything.seeing as the files are decrypted/edited already, there is no real reason NOT to edit just a tiny bit more and make it region free.
keeping them not region free will not help you in anyway or make the game any different
no need to keep an old version of the program
Edit: anyway the 3.1 works great, the only thing useful for me in the new release is the download play support, but i can easily use another tool for that few games