I've updated several CBHC installs without issue. The only thing I can see messing you up is during the upgrade did you choose the wrong DS game? If your correctly chose the right DS HaxChi game during upgrade you should have no issues.
Again. All user error. We have successfully narrowed every CBHC brick down to user error. If all you did was upgrade your CBHC and didn't do anything wrong and now you have a brick, this would be the first documented case. We need more info.
I've seen where people set up 2nd HaxChi's for various reasons. I see nothing wrong with this. It works fine. You just need to be more careful when you are messing with CBHC. It will ask you which DS game to use. You, the USER must know this. CBHC can't tell if it's legit or not.
Yes CBHC has risks. Just like every other major console hack in history. If you're not sure what you're doing, ask for help first.
I have 4 HaxChi installs. 1 for CBHC (legit eshop purchase) and 3 others for gamecube games on wii u system menu.
It all works perfectly and I have updated CBHC every time just fine. You just have to make sure that you choose the correct DS game during CBHC upgrade.