Hello Aspirant , hope you are doing good.

So, to be able to appear for the JEE Mains counselling, you have to have passed your class 12 examination, or any other qualifying examination, so the fact that you have a supplementary exam this year, you have to pass that first before you can appear for the counselling, or you can reappear for the exams next year after  passing in your supplementary subject.

Hope this helps you. Good Luck!!