Never Should Have Filed 5500

A client brought us a one participant plan that filed 4 years worth of 5500s electronically late (they received bad advice that they could transmit them electronically and then do DFVCP instead of properly mailing them in).  When I looked at the asset amounts, the plan never had over $250,000 in assets.  This money was all cashed out this year and a final 5500 is due for 2021 regardless of the mistaken "late" filings.

My question is, to try to help this client, do we electronically file the final 5500 and then send the IRS a letter that they never should have filed in the first place until now, and here is the final, or should I just mail the final 5500 to the IRS with an explaining letter?

The closest I found to answer was this very old post:  

Jennifer D., I'm not sure of the best course in your situation, but in a somewhat similar situation (actually, more like the "Exempt Entity Filed in Error" situation that you link to), the client, a governmental entity, did get a letter from IRS assessing penalties for late filing, but we wrote a letter and called IRS explaining the plan's governmental status, and it went away. Took several contacts over several months, however. So my guess is that if nothing else works, if the IRS and/or DOL does eventually contact your client assessing penalties, your client will eventually be able to explain the facts and get relief, assuming the facts are as you state.