Thank you for you question about the BRP issue you have.
The Home Office website, see below, states that you must inform them of any change of circumstances such change of name. You partner has changed her surname.
However, I do not think it is a problem. When you apply for your wife's extension visa, the application form should request details of all names previously held. Also provide a brief explanation as to why you didn't inform the Home Office of the change of surname previously. This should not be an issue at all.
I wish all you the best for the future application.
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