1. If he is executing the supplementary agreement which the bank would recognise, then you can proceed.
2. You may enquire the same from the bank.
3. If the supplementary agreement is not by registered deed then no additional stamp duty will be required to be paid.
4. You are right.
5. The stamp duty you have already paid is for regularisation under the amnesty scheme, hence you may have to pay stamp duty for registering the supplementary sale deed.
Alternately you can make your brother as a confirming party in the registered sale deed you would be executing in favor of the buyer, which should be acceptable to the bank for sanctioning the home loan.