When you pay 0.5% stamp duty on an Assignment Agreement sale consideration under Article 5E(ii) of the Karnataka Stamp Act, this amount is generally considered an advance or part payment of the stamp duty. According to the law and prevailing practice in Karnataka, the 0.5% stamp duty paid on the assignment agreement is adjusted against the total stamp duty payable at the time of registration of the final sale deed (which is usually around 5% of the property value).
This means when you go for the final registration, the stamp duty already paid on the assignment agreement should be deducted from the total stamp duty payable on the sale deed, and you should not have to pay the full amount again.
The e-stamp certificate clearly indicating "Assignment Agreement – Article 5E(ii)" confirms that the stamp duty was paid on the assignment, making it eligible for adjustment.
If the builder refuses to acknowledge this adjustment, you are legally entitled to insist on it, and the bank’s view is correct. You should keep all receipts and documents related to the 0.5% stamp duty payment safe, as they will be required to claim the adjustment during registration.
In case of dispute, you may seek legal advice or intervention to ensure your rights are protected and avoid double payment of stamp duty.