Export bill recorded in gstr1 but not in gstr3b

can you tell me 

you want file refund montly basis or quaterly

If u want file refund quaterly  then u can show export invoice in next gstr3b 

 and u can show firc of export invoice in SO3 template and u can file for refund

yes we have already filed GST refund but we have received query from officer that they getting difference for same amount so is this effect our refund amount?

no...the amount is same as per shipping bills