Invoice difference in E-way bill & Gstr-1

IGST wrongly applied on Export invoices when generating E-way bill.

However, rectification was made in GSTR-1 by filing Export invoices under 'Export of Goods With Payment of Tax'

Now department has mailed us about the non payment of IGST and has asked us to pay the tax. But no official notice has been issued to us.

What should be done now?

Please help