i am unware of the commodity you are dealing in, in such commodities where so huge amount of moisture and evaporation is done, you have to use excise sealing,
are your range officer and department aware that this much 8% materials go vanish in moisture? if yes then you have to clear additional quantity to cover up your consignment where the R/O would allow moisture surplus without payment of duty, under excise seal
in any case the quantity can not be short shipped of what is mentioned in ARE-1, or it would be case of en route diversion of taxable goods, which is evasion in eyes of department.
Shippinng bill (EDI), how did they ascertain the quantity ? it was the declaration of your CHA on the basis of which they prepared the shipping bill, coz they dont have any system to measure your goods prior to customs check point., in this case they had to book shortage in quantity, and allow the short quantity by making correction endorsement on shipping bill.
your invoice / packing list, .........................when it got changed ? if prior to export you changed it............. why not u did informed Range officer regarding shortage of materials due to moisture, and obtained certificate in this regard to get reconsilated at customs port? then the shortage of ARE-1 would not appear.
undertaking as the word produce itself, where the manufacturer is obliged to pay the diff of duty of materials getting short between quantity actually cleared from factory and quantity actually exported.
Indirect taxes should not be handled at par with vat or income tax, as the penalty provisions of indirect taxes are bitter,
in case of any deviation, mistake, error, intimate your Range officer under signed acknowlegemen, so that in case of any trouble next, u can get a safe side that you have intimated the R/O in due time and R/O is aware of situation, this would save you with bitter experience of "facing anti evasion team"