That's a really strange question that you have asked. I would like to know further details like why would authorities do that? Why would they cancel your jee mains application? If such a thing happens then you will definitely get the access to the confirmation page for your application fee payment. There's nothing to worry about the fee payment. But if such a thing happens you may not get your fee back as this solely depends on the policies decided by NTA and the terms and conditions you may have agreed on to fill the form.

Hope that you may not face such kind of problem and good luck for your mains.