You didn't say how old the plan is, but I'm assuming more than 5 years. The restriction limiting benefit accruals does not apply for the first 5 years of the plan. I'm also assuming there have never been any distributions from the plan or amendments increasing liabilities, so the only concern is the restriction on benefit accruals.
What you might do is certify the AFTAP now, then amend the plan to reinstate the prior years' benefit accruals. If you are already restricted for 2021 because no AFTAP was certified before October 1, then wait until January to amend. If you feel this constitutes a significant qualification failure, and it has been more than 3 years since the restrictions should have first applied, then have the client file VCP.