You don't need to worry about uploading certificates. You can upload certificate during the counselling process. A notice has been put up by JEE Advanced authority,

" Due to COVID-19 related restrictions hindering the issuance of various certificates in time, valid category certificate(s) may be uploaded at the time of reporting after seat allocation. Accordingly, certificate upload portal will be enabled for document upload at the time of reporting after seat allocation. For details of seat allocation schedule, visit JoSAA website (https://josaa.nic.in/) ".

Hope you understand. All the best.