its safe, update. if you used a fail updater (called a "safe" updater by devs), then it'll update boot2 removing bootmii if you have it. Just reinstall it afterwards. It will not remove anything else. 'cept maybe cIOS if you have it.
And every time I hear about Nintendo's or Disney's new legal shenanigans, I imagine legal ninjas throwing C&D letters delicately folded into throwing stars.