In the VAT payments due screen, under filed returns I have one from 31/12/2018 which isn't showing as paid, which it has been. I migrated to Quickbooks online from the desktop version in April when MTD came in and all the other returns from 2015 onwards are showing as paid. Is there a way I can clear this payment?
You'll have to make an adjustment for the transaction that shows as unpaid. This is to correct the reporting method. For this process, it would be best to reach out to your accountant so they can guide you what accounts are to be used. You can take a look at this article on how to make an adjustment: Adjust your VAT liability.
Also, they're the best support that can decide whether there's a need to delete the other returns from 2015 and onward.