CO once deleted a MFE-IAH flight from an itinerary for me because I wanted to take the bus across Texas and see what was there. (On a deep-discount ticket.)

I think the agent decided I was dangerously insane and should be humored to avoid disaster :-)

Mind you, I had been doing that route a lot so it was probably obvious from my history that I wasn't trying to scam the system which may have helped.