yes you can do that. but i would just backup the "Interface" and "WTF" folders which is on the SSD and work on it from there. you'll benefit from the load times coz i imagine you'll be doing quite a bit of this -> "/console reloadui"

before i start mucking around, i also take a screenshot of the current UI and other important configurations so in case something goes wrong, i could still recreate the look and feel of the old UI.

gl.