N.Y. Comp. Codes R. & Regs. tit. 20 § 3-2.6
(Tax Law, sections 211(3), 1083(c)(7), and 1087(c)(1)).
If the taxpayer files a report or an amended report as required by section 211(3) with respect to an increase or a decrease in Federal taxable income or Federal tax, or with respect to a change, correction or renegotiation of tax that is treated in the same manner as if it were a deficiency or overpayment for Federal income tax purposes, or with respect to a computation or re-computation of tax that is treated in the same manner as if it were a deficiency or overpayment for Federal income tax purposes, the amount of tax attributable to the Federal change, correction or renegotiation, or the computation or re-computation means the amount determined by recomputing each of the alternative tax bases for measuring the tax imposed under article 9-A, taking into account the item or items resulting in the Federal change, correction or renegotiation, or the computation or re-computation for the taxable year. Such amount shall be computed without change to the business apportionment factor (BAF).
N.Y. Comp. Codes R. & Regs. Tit. 20 § 3-2.6