Thank you for the reply. Sadly, this doesn't resolve our problem.

The accountant we used to help us re register for VAT ended up creating a second Government Gateway account for the VAT accounting. You've confirmed my fear that we can't use two G.G. accounts in parallel on QBO and we now have a VAT return due and no way of submitting it.

I've gone into the QBO settings - Account and Settings - Payroll - Online filing with HMRC - and have inputted the alternative VAT G.G. login info to see if I can alternate the G.G. accounts on QBO but that doesn't seem to have worked either.

Is there somewhere else in QBO that registers the G.G. login details?

I have verified the correct VAT no. is input in the VAT settings   

Thanks for your continued help and Happy New Year!