Gov.uk verify will shortly be retired and will no longer be in use. There are due to be changes to the identity verification journey for Government Gateway, which will be implemented in July.
If an accountant is going to be completing the tax return for your wife, they will have their own agent account with HMRC through which they can submit online returns.
If there are issues with the certficiate your wife can discuss this by calling our Income Tax team and they can refer her to the taxes technicians who can advise further.
If you wish to make a complaint you can do so by telephone or in writing:
Make a complaint about HMRC