Would running bowl cleaner through a piece, cause it to lose the color changes it got from being used?
yes i think it might do something to the glass. i would just use some rubbing alcohol. if its really packed with resin you can soak it in rubbing alcohol for a while. usually for me though i just run hot water through it until it all comes out.
The color comes from the resin buildup, so if you clean that the color is gone. If you smoke again the color will start comming back. At least that's how it's been for every color changing glass piece i've had.