Scheme Certificate matters only when you have had a service with any previous company or companies. Scheme certificate is issued when you change employment and withdraws the PF amount only without withdrawing the pension amount. Obviously, if you had 10 years of service, you cannot withdraw Pension Fund but the only alternative is to get a scheme certificate from the EPFO which certify that you had so much of service, your last drawn salary was so much and also give details of your spouse and children who are eligible to get pension in the event of death of the scheme certificate holder. Normally, this is surrendered when you join another organisation and with this your past service will be added to the new company.
While applying for pension, if you have scheme certificate, you can attach the same or if you do not have any scheme certificate, just ignore it.
Please reconfirm whether pension application is made online. I think, the pension application is still offline only but with reduced documentation.