Hii Harshit!
Do not worry about that. Just focus on your studies and do well this time. The more you work smart the more marks you get. So, have confidence on yourself that you can get good marks. And, coming to your question, even if you get less marks in one subject, the best out of the two will be considered and will be reflected in your marksheet. So don't worry and study well.
Hope this helps.
Good luck!