The biggest "risk" is a failure during the transfer (a reliable wifi network helps, so does carefully following all the steps), in which case the hacked save may be lost and you will have to start over (possibly being subject to the week of waiting, depending on whether Nintendo servers considered the transfer completed)
Licenses of your digital games and any NNID (logged in or not) will also transfer, but frankly it's not a big deal considering you can create and install backups of your games/dlc, pokebank/badge arcade are ripoffs with free legal homebrew alternatives, and you can create another account if you really want miiverse
Any software/saves/extdata on the receiving console will be erased, but this is the system transfer working as intended, even Nintendo tells you this with an entire page in the manual and the transfer process