No. I deliberately wrote HeXEn to make as few changes as possible when updating softmods. It made the scripting loads harder, but means that things like existing apps won't be touched.
There are options on HeXEn that will wipe your disk and start from scratch, but unlike all other rescue discs they are all passcode protected and have at least one "are you sure?" dialogue box to minimise the chances of you wiping your system accidentally.
The options you need don't wipe your E or F partitions, which is where your emulators should be. Options 2.1.x or 2.2.x install a clean softmod, so they replace C, shadow C, the dashboard files on E: (E:\Dash\ or E:\Dashboard\ depending on if you choose Krayzie or Kingroach), and the exploit gamesave files in E:\UDATA\ (but they leave all other gamesaves alone). They add a couple of small folders with some management tools, but nothing that would interfere with any Emulators you have installed on there.
The only limitation is that you need around 200MB free on E before you start, so if you've absolutely filled your E:\ partition with emulators then HeXEn won't work. I say "might", because if your softmod installer already took a copy of the stock C files then you don't need 200 MB, you only need around 10-20 MB (I can't remember the exact number, and can't check because I'm on a train!). In passing, it's also worth noting that it is recommended always to leave around 100MB free on E for the Xbox to work properly. However, don't worry - HeXEn checks for free disk space, and if there isn't enough space it aborts the installation before making any changes - yet another little user-friendly bit of scripting to make everyone's life easier.... This post has been edited by Heimdall: Aug 3 2011, 10:00 AM