Last time I saw a CP2000, it specifically instructed NOT to file an amended return.  Just respond to the notice.  IRS is a big place and the people who audit returns are not in the same office, or even the same city, as the people who process amended returns.  

IRS says amended returns filed in March are being processed now, so maybe a hold has been placed on the CP2000 until the 1040-X is processed.  Or maybe they have put a hold on the 1040-X process so they can finish the audit based on the response.   This was a 2022 return? When was the CP2000 sent?  Most of those would have gone out by last July.  

Form 1040 series

• Original: April 2025
• Amended: March 2025