If you do have to paper file, then I recommend having the client mail it in Via USPS certified mail with return receipt. I have at least two 990 clients who paper filed a few years or so ago before the e-file mandate, and they received letters from the IRS that the returns were not filed. Letters were sent to the IRS with the certified mail documentation and the matters were resolved. If you do paper file you may also want to consider attaching an explanation as to why you did not electronically file.
