No, It will not create any issue. The best marks will be the scored marks as Best of 2 will be considered.

Your Percentile based on category is: 95.2 - 95.4

Your Overall Percentile is: 85.65 - 85.85

Your Rank based on category is: 1425 - 3075

Your Predicted Rank is: 130248 - 162398

I will recommend you to check All The Colleges, That is available for You on basis of your rankings and Reservation, Then You can also check that at Our JEE MAINS COLLEGE Predictor. That will be very helpful for You.