IGST NOT SHOWN IN SHIPPING BILL BY CHA

In an export to Nepal the CHA on Shipping bill has shown IGST as 0 whereas we have charged on the tax invoice.

this tax invoice (not commercial invoice) details are only coming on the shipping bill

They wrongly selected Lut option whereas we don't have LUT.

they are asking us to file showing IGST as 0 on GSTR1 

should we do the same ?

if we show as IGST sale can we claim this IGST amount as loss since we will not get refund for it due to shipping bill and tax invoice mismatch