Unfortunately late filing of your annual CRO return will still result in the need to have accounts audited for two years. A change in company law in 2018 does allow some concession however.
A company that files its annual return late will not lose its entitlement to an audit exemption in respect of that year, but will instead lose it in respect of the two following years. So all it really does is push the problem down the line.
So the lesson is DO NOT MISS YOUR CRO FILING DEADLINE.