Filing divorce will not affect your 498A.
But the think is you may not get divorce since to get divorce you need to prove -
Adultery / Cruelty / Desertion / Failure of RCR / - - - - - etc out of anyone properly. (Please see Sec 13 of HMA for details)
These are very hard to prove in the court.
Secondly, If you file divorce during 498A trial then the judge will be more sympathetically see your wife and may order very huge maintenance U/S 24 HMA and 25 HMA. If you don't pay this maintenance the case will be in suspended stage. Also there will be risk of DV.
Please file speedy trial and get 498A dispose of first.
Then you can easily prove Cruelty and Desertion and get divorce.
Please see my post in the following link: -
https://www.lawyersclubindia.com/forum/details.asp?mod_id=103100&offset=3#.U49QYHbYVdg