This would be a good idea on a custom updater. All you have to do it put the RomFS or CXI file in a folder in the root of the SD card. Next, open up the updater to check for updates and check the current version of the game installed, then if there is an update it will download the files and will rebuild the RomFS in the 3DS. When it is done it should replace the rebuilt RomFS with the current RomFS. Well, you can make this if you want to or if you have the time for it. This would just help save some time.