You can submit your end of year form, and it will be processed. However, pension records can only be updated sequentially.
This means that, if any certificates from previous years are missing, contributions for the most recent years will not show on the NHS Pensions system.
For instance, if a certificate is missing for the year 2015/16 then the Annual Benefit Statement will only reflect the pension figures up until 2015, even if the certificates for more recent years have been submitted.