IRS requesting refiling for lost return

Client , a non-profit entity , just received a letter stating that the IRS does not have the required 2019 form 990 return. The return was properly filed in the second half of 2020 and  client has the certified mail receipts. (At that time there was not e file mandate for form 990 as there is now). letter States, among many other things, that if you have already filed the required return more than 4 weeks ago to complete the response form at the end of this notice and mail it in the enclosed envelope with a signed and dated copy of the return. The response form States and asks if you already filed that you are enclosing copy of the return and they ask for the date the form was filed. So it looks like the original return that was filed and received by them cannot be located and now the client has to file a copy of the return.... hope this information is useful for others and if anyone else has advice or a similar situation please share it with us....