How to reconcile self assessment tax if challan is misplaced

I received an intimation from the authorities for my return for AY 14-15 that I haven't paid the self assessment tax, and a penalty has been applied. My tax returns and tax payments are done by my CA who has proved to be incompetent and negligent. He cannot trace the payment challan. In the Itr I found that he has quoted the same challan number for both advance tax and self assessment tax paid by me. But the payment of self assessment tax has been debited from my bank account and shows clearly under SBI IT. This is the only proof I have. I have appointed a new tax preparer now. Kindly advise on how I can solve the problem, as I will end up as a victim of double taxation