The disc updates dont actually overwrite your softmod, it just simply removes them but not all. It even says in the manual for the game that any modifications to the console could be erased. So it obviously removed your bootmii application. This is why you should never do a nintendo update if you softmodded your console in any way. It wont brick the console but you can lose some if not all homebrew applications. In your case, you lost bootmii. You actually could have lost more but cant see by looking at it. There are times when you wont lose neogamma, but youll lose ios249 and the cios you had installed. The only time when updating through nintendo can be done without any side affects is if you just have a modchip and no softmod done at all. If your console updated to 4.2, your lucky it didnt brick. Nintendo's 4.2 update can detect softmod console and purposly bricks them.