Gst input not reflected in 2017-18 , due to reverse charge option wrongly selected.

Dear All,
could any please help with,
As we are in receipt of our customer/ dealer query. he was in receipt of gst notice for gst payment for the purchases done with us in July' 2017-18.
He auditor claims that, we have wrongly opted the reverse charge option while filing the return during the period.
When I interacted with our tax team, he told that , return amendment period was closed. Hence we cannot reimburse the gst payment to him.