Brewology

I have homebrew channel and hackmii installed into boot2. System Menu Version 4.2. I have used another way to update the wii to 4.2 without boot2v4 or any unimportant things.
I want to update normally so I can properly update Wii Shop Channel. Apparantly the homebrew updaters for those aren't working that well I hear.

So if I update normally, will this install boot2v4 or does it think it's already installed it and wont install it?
Also with the IOSes checking for wii mods and all. Will this have any effect on homebrew or negative effects on the wii because i'm not seeing any infomation on wiibrew.org about this.

ok you have HBC check, Bootmii as Boot2 Good, make a backup, Also Xtreme09 Just use a Shopping Channel Updater there are many, maybe not 1 yet as it was another shop update was done yesterday, To be honest just wait like 3 days for one to be out, i would rather wait 3 days then maybe a few years to remove boot2v4.