Bank not refunding amount deducted before payment of loan. What to do?

SBI, RACPC, Howrah accorded sanction of Home Loan of Rs.9,50,000/- on 30-04-2010 for purchasing of complete residential Flat. I had informed AGM, SBI, RACPC, Howrah vide letter dated 25-10-2010 regarding the registration of flat on 29-10-2010 and requested him for preparation of a cheque of entire loan amount in favour of Promoter. Consequently, RACPC, Howrah handed over to me a photo copy of a cheque of Rs. 9,50,000/- in favaour of Promoter. Due to unavoidable circumstances, execution of deed was not done. In this context, the bank was intimated with request to cancel the cheque at that point of time. Bank had started recovery of Principal & Interest from Nov’2010 through my Savings Account without disbursement of loan. Factually, my Home Loan of Rs. 9,50,000/- was only received and disbursed on 09-10-13 through Fresh Cheque in the name of Promoter. Bank do not want to refund or adjusted of Rs. 3, 76,473/- which was deducted before disbursement of loan. What can I do. Pl. advice.