IRS letter

Hi, Owner only DB plan received letter that his plan has been selected for examination. The exam seems to be just that the IRS did not get his EZ for 12,13, and 2019 (for location and date it says N/A). The agent says that he should file the missing EZs with the delq. program, however, it must be sent to the agent (as opposed to filing directly DELQ. program). The 2019 was just  filed on October 15th, 2020. The other years as well. I recall that there was mention that there isn't anyone at the IRS location to process the 2019 EZs.  Thank you.

To clarify the above, if the  5500-EZ for the years that the IRS claims they did not receive were actually filed, why should the sponsor have to pay fees for the Delinquent filer relief program? The sponsor even has a copy of the October 15, 2020 postmark for the 2019 filing.