Inter unit transfer - Customs - Exim - SEZ

Sir, An EOU unit has supplied goods to another EOU (inter unit transfer) for last 3 year has has not taken prior approval from Development Commissioner as well as from customs authorities. The recipient unit has not issued form-A also in this regard. Since the recipient unit is paying IGST to supplier and availing ITC. Now the Development Commissioner and customs authorities are of the opinion that such transactions cannot be treated as deemed export as per FTP and therefore the supply will not be calculated for the purpose of NFE. Now if the transaction is not calculated for NFE, my NFE will not be positive. Can the authorities disqualify this transaction as not treating as deemed export under FTP, just due to procedural lapse.