You can use that button, just make sure to do all the changes you want on the character tab and press it *before* editing your skills, otherwise rewrite the character node.
Sorry, I phrased it badly. What I meant to say was "Do not use "save all changes" button AFTER editing skills". You're right of course.
Thanks for the tool, it is amazing. One thing to note: I wasn't able to unpack Textures_2 and Textures_3 pak files, the editor complained of version mismatch (expected 7, found 9).