Dear student, here's the list of document that you will need to provide during the counselling-

• Three Passport Size Photographs identical to the one Uploaded in JEE Main 2019 Registration
• Provisional Seat Allotment Letter
• Candidate Undertaking
• Proof of Fee Payment by e-challan or Internet Banking of SBI for Seat Acceptance (Rs. 15, 000 for SC/ST/PwD candidates and Rs. 35,000 for others)
• JEE Main 2019 Score Card
• JEE Main 2019 Admit Card
• 10th Standard Mark Sheet or Date of Birth Proof
• 12th Standard (or equivalent) Mark Sheet and Pass Certificate
• Photo Identity Card
• Medical Certificate
• Category Certificate (if applicable)
• PwD Certificate (if applicable)
• OCI Certificate or PIO Card (if applicable)
• Print out of Filled Choices for Seat Allotment

All the best 

Hope this helps 

It is better to provide all the required documents at the time of registration. Try your best to collect the damn certificate. But don't panic, if you don't have it now your admission won't be cancelled, you can provide it later also but its best to be prepared with all documents. Don't worry much.