As you noted, an IRS Notice CP-406 is from the IRS. You should find this link very helpful in sorting out steps to take in response to the letter:
https://www.irs.gov/retirement-plans/irs-filing-notices-for-forms-5500-5500-sf-5500-ez-or-5558 particularly in the section titled Understanding your CP403 or CP406 delinquency notice in subtopic Is there any way to reduce late-filer penalties?
Basically, the advice is to file under DFVCP. The DFVCP process is very user-friendly. Only 2022 form is late if the 2023 form was filed on 10/15, so amend the 2022 form and check the DFVCP box. Note that filing an amended form replaces the prior filing in the EFASTs system which should make it unlikely that the DOL will initiate an assessment. You will need to do this before using the DFVCP penalty calculator since it will ask among other things for the EIN, plan number and date the form was filed. The DOL uses this information to cross check the form filing to the form filings listed in the calculator and will expect the 2022 form to have the DFVCP box checked.
Both agencies really want us to use these delinquent filer programs and they commonly respond well to a plan taking proactive steps to correct an issue.
Good luck!