I think that is the nature of CandyBar unfortunately. When I have run into that on occasion, I just revert back to the manual way to change icons that was used before CandyBar and LiteIcon made it easier- that being (skip this if you are already aware of how! 😉):
Use File-->Get Info on the icon you want to use and then the same on the application you want to change
Click the small icon in the upper left corner of the icon's Get Info window to select it, then press Command+C to copy it.
Click the small icon in the top left of the application's Get Info window to select it, then press Command+V to paste in the custom icon
Close both windows- done.
Less convenient than using CandyBar's functionality, but infinitely better than reorganizing the whole Apps folder-- particularly since some app updaters require the apps to reside in the folders they were initially installed in.