You can freely update the BOBCACHIEVEMENT_LIST list in your new build. It will not affect anything with existing unlocked achievements or saves, or anything from previous builds.
(If you remove achievements from the list, it will remove them from display on the screen, if you're using it, but it won't "ungrant" the achievement to anyone that had already achieved it.)
If you're releasing on Steam, remember to add any new achievements in Steamworks as well as updating the BOBCACHIEVEMENT_LIST list.