I had to do a lot of work to this car so ill start with going front to back and stating what was changed or fix as I go along this thread
after the keyless was working again had to get a spare key made, Honda 3S advised against ordering a new key from them as they and I am quoting Honda Fort here said that last time they were unable to mate a new virgin key with the car and it was unsuccessful. Honda defense also refused to order saying price can vary from Rs. 35,000 to Rs. 75,000 and last time they placed order at Rs.35000 but end price from company at time of delivery after two months was coming Rs. 75,000 for a single key so they advised not to order either.
this was stupid, Honda 3S after sales for accord is worse than any German after sales even if you take any grey market car to them they can still order parts.
in the end found a guy who does Range Rover and German and other cars key and he sourced me a virgin key came to home and reprogrammed it to the immobilizer using his scan tool and also cut it according to the locks and voila I had a new working key which operated everything and only costed Rs. 10,000