Also i found out in unpleasant way that when you load the save that you make at the end of the chapter, it doesn't load correctly. So basically i lost my progression TT.
Edit: My bad accidently loaded jap version. Everything's fine
FrantzX's tool extract those files in different format, so it's not gonna work. But as far as i remember somewhere in this post there is a iso builder tool that can extract and then build back an iso file.