I just took on a new client, they have 2 years financial statements outstanding (2016 and 2017) and the last set of accounts filed with the CRO was late. If I apply to the District Court to extend the filing deadline for the annual return as permitted under Section 343 CA 2014 will the company be eligible for audit exemption for the two years set of financial statements still to be filed?

No if an application is brought before the courts under Section 343, while the late filing fees will be waived assuming the application is successful for both years, for the 2016 financial statements, these will still have to be audited as the Company was late in filing the annual return in 2015 and as the annual return was late in that year under Section 363 CA 2014 the 2016 financial statements must be audited (as you lose audit exemption for 2 years – the 2015 accounts would have been audited when the annual return for 2015 was filed late and the 2016 accounts will now have to be audited). The 2017 financial statements can be audit exempt as by then the 2 years of audit will have elapsed due to the late accounts being filed in 2015.