Vat refund - lr missing - can sales tax office reject the refund?

Hello We had filed a refund application for VAT. For processing the same sales tax officer has been repeatedly asking different documents. We have supplied most of the documents (C form, H form, purchase order etc) We provided LR (Lorrie receipt) for most dispatches but we have lost LR of 2-3 dispatches. My question is: 1) Can sales tax officer reject FULL refund application paying nothing? 2) Isnt C-form not a sufficient proof? 3) Will we have to pay difference amount between VAT and CST? (about 4%). Even if C-form was issued? 4) Can there be interest and random penalty? Or there are rules for such cases? Our CA who is handling the case says that we may have to pay difference in tax plus interest and plus 100% additional penalty. All these just because we have lost LR copies does not sound like justice. If anyone has a solution then please guide. Thank you.