Kim held Dan's dick by the head, and saw that it was purple and starting to swell, there were at least two tight knots in the shaft and his testicles were wrapped around one another. It was a complete and mangled mess and not one Kim could fix on her own, she either needed a doctor or she needed to transform it again.
Not wanting to explain this situation to a doctor she went back up stairs and opened up the Chronivac. There didn't seem to be an option to restore them to their original shape, all it would've done was attach the mangled mess to Dan. Thinking of Dan she hoped he couldn't feel this. Luckily there was a delete button and while she felt guilty and getting rid of his genitals, it was better than their current state. So she hit the button and Dan's genitals vanished from existence.
She then looks through the program again looking how to get Dan his dick back, hoping she could undo the damage.