We are in the same boat and realise that HMRC will probably be unsypathetic. We have employed a solution. We have downloaded a program from "Anna", a company that has a free vat return template, which downloads into Excel. Once downloaded you fill in the 9 VAT boxes on their template, and through the Anna icon you gain access to HMRC, authorise the Anna program which puts you back to the Anna template , this then allows Anna to submit on your behalf.
It's called bridging software and its free, it also creates vat records future inspection.
Did it today and it works๐๐