LOL, gotta love dem updates.
Now I'm not sure what all you have access to with your way of exploitation, but you could simply move all your save data to a usb and do a factory restore to take you back to the first firmware you were on. Since the console has the same signature no matter what firmware you are using your save files should be safe.
So in short theoretically you could take off your save files, upgrade your wii u, download your game to a hard drive, remove your hard drive, then do factory restore, then use disk to upgrade. I don't know what will happen with your MII character though. Also if you have complete access to the console via your browser exploit then you should be able to capture the update and spoof it. (or whatever else you may want to do with it)Personally I am considering doing a factory restore just to see what other holes were missed in the earlier firmware. (I have two, one from release day nov. 2012 and one from late 2013<--not doing anything to this one)