The head will come as a bare head and they will transfer the cams, valves etc over. They might be replacing it for clogged secondary air ports. this will cause a check engine light but should not cause any rough running issues. It could also be that a valve seat was worn or damaged in this case you would get a new head and valves but they would still transfer over your old camshafts, lifters and rockers.

Sounds like your service advisor probably doesnt have all of the information or just doesnt understand the technical side of it. Feel free to call him/her back and ask for a better description of exactly what they are doing on your car. If he cant clearly explain it to you then ask to speak with the shop foreman or the tech who is working on the car so that they can describe to you exactly what they are replacing and why. Its your right to know.

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DT