Yes usually they replace it. If it was done at a dealership then I would assume they replaced the pilot bearing, throw out bearing, pressure plate and clutch disc. This is usually sold in one set.
So, you said there is a noise present at idle and if you depress the clutch pedal, that noise goes away? Usually that is a sign of the input shaft bearing falling on these hondas. Almost every high mileage honda manual transmission i've seen has signs of this noise. It almost sounds like someone is skating inside your transmission.
Is the noise at idle, the same type of noise you are hearing when you accelerate?
Sunday, December 7th, 2008 AT 7:17 PM