At the time of registering the Sale deed, payment of Stamp Duty, and registration Charge, it is highly unlikely that the deed number is not generated. The deed number is written at the top of the sale deed in this format 5427/2018/HVL1. Additionally to this, the payment receipt mentions the Registration Number, and also on each page of the Sale Deed a stamp is put by the Govt authorities giving the Registration number, page number, and the total number of pages in that Deed.
Yes, you would need to pay the stamp duty and get your sale deed registered as per the revised rates, as you did not get your deed number when the sale deed was being registered.
Since you mention that you have already paid the stamp duty, you may request a waiver of stamp duty, based on the stamp duty already paid, by making a representation to the registrar and putting forward your case and they may adjust the stamp duty paid earlier with the difference of stamp duty to be paid now.