I created a wonderful GitHub Pages website for my little project, and I added some other pages into the gh-pages
branch.
My problem is that, everytime I regenerate
No, not possible. GitHub wipes the gh-pages repository when you do a "generate". Best you can do is what you are doing now. Another option might be not to use the GitHub page generator to change styles, but to find the source of the styles (they're probably on GitHub somewhere) and manually change them by committing changes (substitute the css files and other minor tweaks)