Thanks for the clarification. I’m assuming that your dad was registered for VAT as a “sole trader”. A sole trader registration can’t just be converted into a partnership registration – see https://www.gov.uk/vat-registration/transfer-registration. This would explain why you and your brother would have needed a new (partnership) VAT registration, the partnership needed to opt to tax the property, and there was an actual transfer of the property from your dad’s VAT registration to the partnership’s – which would have been treated as the transfer of a going concern.
But, I still think the position now is different. The link in my previous post implies that removing your brother from and adding your wife to the partnership won’t require a new VAT registration. In which case there is no transfer of the property between VAT registrations and no new options to tax are needed. Your option to tax would have been made by the partnership, and it will continue to apply to the partnership even if individual partners change.
The transaction between you and your brother wouldn’t appear to be a supply of the property by the partnership, therefore it wouldn’t be affected by the partnership’s option to tax.
So I think all you need to do for HMRC VAT is the VAT2 form to change the partners in the partnership.
However I have been making some assumptions about the arrangements. So if your accountant knows and could recommend a VAT advisor, you may want them to give you a written opinion having seen all the relevant documentation, just so that you have something you can keep on file. I’d imagine it should be relatively straight forward for someone with experience in this area, so shouldn’t be too expensive. Alternatively of course, just printing and retaining a copy of this forum thread would at least show that you took some steps to establish the VAT position, should you need to demonstrate this in the future.