I have a 13 year old Accord and one day both keys refused to turn (the black ones. and since I was outside I did not have the gray key with me). I towed it to the mechanic. He took the column out and replaced the worn pins. All the keys are still intact. He then told me, other than his labor cost, he needs to charge me $100 for programming the keys by Honda.
My question is, if the keys are not replaced, why would they need to be reprogrammed?

Another problem: while the two black keys now work, the spare gray key would not turn since it is a thicker key. The mechanic did not ask for the gray key and he did know about it. Does this mean the cylinder takes two sets of pins?

Thanks in advance for any advice.

 

http://www.hondata.com/immobilizer.html

The transponder codes in the keys must match the codes in the immobilizer and match the codes in the ECU for the car to start

It sounds like he replaced the immobilizer system itself. This means he does need to reprogram it. $100 sounds fair.