Society creating issue can I make affidavit or confirmation deed

Sale deed between bro was made in 1993 and was not registrated and stampduty was not paid , on that base the falt was trasfered to the elder bro and the indiminity bond was also made at that point which help all the documation. now after 23 year the society is creating a issue saying u r not the owner of the flat but a nominal, we have put all the document for aducation department to pay stamp duty proceeduer but still therewating for the reply, now the thing is that the younger broi poassed away now i want to knw should we make a affidavit or go for a confirmation deed