Why do you have to update?
My recommendation is enable priiloader hacks to stop disc updates, then if the game crashes you most likely need to update an IOS, to do that firstly search GBAtemp/create a new thread. Then use NUS downloader to get the IOS, install the wads and it should all work.
Attached Link:
http://filetrip.net/f12050-NUS-Downloader-1-5a-Beta.html