N.Y. Comp. Codes R. & Regs. tit. 20, § 8-2.7 – Limit on amount of credit or refund.

(a) after the mailing of the notice of deficiency; or
(b) within the period which would be applicable under section 8-2.1, 8-2.2 or 8-2.3 of this Subpart if, on the date of the mailing of the notice of deficiency, a claim has been filed stating the grounds upon which the Tax Commission finds that there is an overpayment.

Tax Law, § 1087(g)

The amount of overpayment determined under section 8-2.6 of this Subpart will, when the decision of the Tax Commission has become final, be credited or refunded in accordance with subsection (a) of section 1086 of the Tax Law, and shall not exceed the amount of tax which the Tax Commission determines as part of its decision was paid: