N.Y. Comp. Codes R. & Regs. tit. 20, § 540.4 – Protest procedure.

(a) Unless the applicant files a petition for a hearing or a request for a conciliation conference within 90 days of the date of a notice of proposed refusal to issue a certificate of authority, such notice shall be final.
(b) Upon timely application, a hearing or conference will be scheduled in accordance with the hearing procedures described in the Tax Appeals Tribunal Rules of Practice and Procedure (Part 3000 of this Title), or the Division of Taxation's Bureau of Conciliation and Mediation Services Rules of Practice and Procedure (Part 4000 of this Title). Provided however, the provisions of section 4000.5(b)(ii) of this Title are not applicable to the proceedings provided for in this section.
(c) Where any applicant who has received a notice of proposed refusal to issue a certificate of authority has made a timely application for a hearing or conference, the applicant's existing certificate of authority shall not expire until such time that the applicant has received:
1. (1) a conciliation order from a conciliation conferee upholding the department's notice of proposed refusal, and such order has become final; or
2. (2) a determination from an Administrative Law Judge upholding the department's notice of proposed refusal, and such determination has become final; or
3. (3) a decision of the Tax Appeals Tribunal upholding the department's notice of proposed refusal, and such decision has become final (including any judicial proceedings applicable thereto).
  Provided, however, such certificate of authority remains subject to the suspension and revocation proceedings described in section 539.4 of this Title.