Sadly your wife cannot claim tax relief, as the property was held in your sole name, so all rental income and associated expenses should be claimed through your tax position.
This will need revisiting for the earlier tax years (if HMRC have not already identified this as an issue) and although the tax liability, will result in a refund on your wifes tax, this then can be used to cover the liability on yours. (of course if your rate of tax is higher than your wifes then this does later matters)
My advise - is it possible if you transfer this property into joint names, then for married couples, the joint ownership is treated as the whole period of ownership, then you only have to concern yourself with the years when she solely declared the income, to rectify theses to 50:50 share.
Sadly the fact that your wife did all overseeing and management of the property, and and another solution your accountant should have proposed is that she was paid for all the work she clearly undertook.
How the accountant can argue he thought the property was in joint names, when all paperwork would have suggested otherwise, and that he sometimes allowed her to declare all income and other years made this a joint declaration, seems a bit odd to me, so another factor is whether you have any redress against the accountant for his mismanagements of you and your wifes tax affairs.
Do feel free to ask any follow up questions, I can see that you did not have a good response initially, but if you could rate the level of service I have provided, it would be appreciated !