Provision for filing of revised vat annual return

Dear Sir,

           One of our client filed the Annual Return VAT 240 in Karnataka Commercial Taxes.Due to some internal problems they have not disclosed the complete details in annual return and omitted the stock inward as well as stock outward.Without considering these two the auditor has filed the VAT Annual Return as well as Trading account.Company has made a notice to the department to regularize the books and requested them for issuance the Form f and submitted the form f for the stocks received from the other states.Unfortunately some of the sales return were shown in labour charges column in VAT monthly returns by the accountant and the auditor incorporated the same in Annial Return by adding the amount in sales turnover.

Now the assessing officer has issued a notice to the assesee to pay the tax for stock difference after netting of all the differences.

Now my question is how the stock outward( Branch Tranfer interstate) can be treated as stock difference even after submitting the form f from the concern state.tax authority.

2.Why don.t the authority treat the labour charges as sales retururns.as the mistake was happened purely by clerical mistake.

3.Why don;t the authority allow the assessee to file a revised Annual return and trading account to regularize the books of accounts.

Please suggest me how to come out of this problem without making any penality.

Regards