Should I apply for the 2nd round with a percentile of 99.233rd at IIIT Hyderabad?

No, I don’t think it’s wise to apply for the 2nd round with a percentile of 99.233rd at IIIT Hyderabad. Based on the cutoffs, the minimum percentile required to get IIIT Hyderabad CSE is 99.78 whereas for ECE is 98.87. Even if you end up getting ECE in the subsequent rounds you will end up losing a lot of money. Moreover, paying a sum of 20k just for a single round is not justified especially when your chances are slim. 

Additionally, only half of the fee is considered an advance tuition fee. So you will lose a lot of money whether you get admission or not. It’s better to try another IIIT or a NIT than IIIT Hyderabad. But if you are adamant, you can surely try your luck!