Tax clearance question

I've fallen behind with my business' PAYE retuns. Does this mean after submitting and paying them in full I will need to re-apply for a new tax clearance certificate even though my current one will still be within the 12 month validity period?

Your tax clearance certificate is still valid for a full year up to the expiry date on it. However, once it expires and you need to apply for a new one you won't be able to obtain one until your PAYE tax returns are brought up to date.