REFUND OF TDS RECEIVED BUT ITR NEEDS TO BE REVISED

Income tax return filed showing Total Income 246000 TDS refundable Rs. 13456. ITR processed and Refund received. But actual Income is Rs. 847000 for which tax liability has arise. Now the question is if I filed revised return then how can I pay the tax which has been already refunded.
It is to be noted that ITR must be revised as Bank is not processing the loan based on the original return as the total income is too low compare to actual income.
Expert view is required.
Thank You.