Yes. Great question. I'm looking at a CP2000 right now and under "Next Steps" it says, "If you are making other changes, we recommend you file an amended return (Form 1040X), write 'CP2000' on the top of and attach it behind your completed Response form."
I have read a lot of discussions where tax pros were unbending on the never file a 1040X in response to a CP2000. I am convinced there are times that it is absolutely necessary, and if it causes more work for IRS that is absolutely not my concern. I'm not going to try explain changes and hope they figure the tax correctly. No way. Plus I either have to do a 1040X or redo the return to know what the tax is myself. Might as well show IRS and not be sitting around for months hoping for the best.