CRA's policy is to vacate the provincial assessment where a federal assessment is directed to be vacated by the Tax Court

CRA has stated that it is "strictly true" that the Tax Court lacks jurisdiction over provincial tax matters.  However, following a successful taxpayer appeal of a federal assessment in the Tax Court, CRA will vacate (or reduce) the provincial tax assessment to match the vacating (or reduction) of the  federal assessment when authorized to do so under a Tax Collection Agreement.  For example, director's liability in s. 227.1 of the Income Tax Act has mirrored provisions in the statutes of each Agreeing Province.

Scott Armstrong.  Summary of 9 August 2012 T.I. 2012-0446051E5 under s. 227.1(1).