House owner (rental) deducting unreasonable amount of stamp duty charges and painting chargeses

Hello.. Im from Karnataka, Bangalore. We have vacated the house after giving 2 month's notice. Monthly rent was 16,800. On vacating owner is deducting 20,000 for painting and cleaning. In the agreement it was mentioned that we have to repaint, if not she can recover painting and cleaning charges from the deposit amount; but the amount of recovery is not mentioned. Requested her a lot to deduct one month's rent which is generally followed. But she said the house is not so cleanly maintained so she wants more money. So i finally agreed. But now she wants to recover stamp duty charges of the agreement. While registering the agreement, we had asked for a normal agreement on Rs. 100 - 200 stamp paper. She said it was for her own requirement and she would bear the charges. And made an agreement for 3,400. Now she says she incurred a loss on this agreement since we ended the agreement before 11 months. There is no clause in our agreement to this effect. Also we didn't end the agreement all of a sudden. We stayed in the same house for 2.5 years; and ended the agreement which was renewed for 2nd time, that too after giving 2 months notice as per the agreement. All the 3 agreements she got done on Rs. 3,400 stamp paper. Though painting this house can be done with some [deleted] i accepted to give up 20,000 for painting and cleaning since because i do not want yo lose sleep over fight with her. But losing another sum in the name of stamp charges seems really unfair yo me. Please suggest what can be done.