If the update has a romfs and uses it, it might just be a matter of rebuilding the update's romfs with the new garc and making sure the exefs in the update is pointing using the path to the update's romfs instead of the normal game's romfs.
I haven't looked at the updates for AS, but for majora's mask, the updates romfs is mounted as patch:/
I've never actually tried this though, so it may be more work than that.
If the update doesn't have/use a rings, then it's not going to be easy because a lot of r/e is going to have to be done to figure it out.