Use ChoiDujourNX to update your firmware and update your CFW before updating your firmware by putting the new CFW files on your SD card.
Well as long as you are not going online with emuMMC, the chances of that happening are very slim. Utilities such as 90DNS and Incognito have served the community well thus far and no one has been banned for either of them failing although some people have lost their backups after using Incognito which resulted in an indirect ban. The point is you will be fine blocking Nintendo communications.
So it seems that you do need to dump something from your Joy-Cons in order to use Android. Whether or not you will need to redump them with a new set of Joy-Cons is beyond my expertise unfortunately.