Charlie is one of our great Head Referees, and he is correct--knowledge and skill loops are mission models, and mission models cannot get a junk penalty for being on the field at the end of the match.
If your team has a detail-oriented rules expert, please note that each of the individual loop models is itself a mission model, so that the removal of a loop from its setup position engaged with another mission model (Search Engine, Community Tree, Robotic Arm, Senses model) is not Model Damage (Rule 30).... unless your robot damages the loop or the other model, of course!
Steve Scherr
VA-DC FLL Referee Advisor