So lets pull this string.
91.213 (d) Except for operations conducted in accordance with paragraph (a) or (c) of this section, a person may takeoff an aircraft in operations conducted under this part with inoperative instruments and equipment without an approved Minimum Equipment List provided--
(1) The flight operation is conducted in a--
[(i) Rotorcraft, nonturbine-powered airplane, glider, or lighter-than-air aircraft, powered parachute, or weight-shift-control aircraft, for which a master minimum equipment list has not been developed; or]
(ii) Small rotorcraft, nonturbine-powered small airplane, glider, or lighter-than-air aircraft for which a Master Minimum Equipment List has been developed; and OK, we are a non-turbine airplane so this paragraph applies
(2) The inoperative instruments and equipment are not--
(i) Part of the VFR-day type certification instruments and equipment prescribed in the applicable airworthiness regulations under which the aircraft was type certificated; CAR 3 airplane certificated prior to March 11, 1996 (more later on this), not part of the VFR day certification
(ii) Indicated as required on the aircraft's equipment list, or on the Kinds of Operations Equipment List for the kind of flight operation being conducted; Don't have a Kinds of Operation List, and the Equipment List would not have Anti Collision Lights as required equipment since they aren't required under CAR 3 and not even listed on the TCDS.
(iii) Required by Sec. 91.205 or any other rule of this part for the specific kind of flight operation being conducted; or Under 91.205, anti collision lights are not required on aircraft certificated prior to March 11, 1996, so not required.
(iv) Required to be operational by an airworthiness directive; and There are no ADs requiring anti collision lights
(3) The inoperative instruments and equipment are--
(i) Removed from the aircraft, the cockpit control placarded, and the maintenance recorded in accordance with Sec. 43.9 of this chapter; or
(ii) Deactivated and placarded "Inoperative." If deactivation of the inoperative instrument or equipment involves maintenance, it must be accomplished and recorded in accordance with part 43 of this chapter; and Must be deactivated (CB pulled and collared, wire disconnected and properly stowed, fuse removed . . .) the switch placarded and a maintenance record entry made by someone authorized to perform that maintenance task
(4) A determination is made by a pilot, who is certificated and appropriately rated under part 61 of this chapter, or by a person, who is certificated and appropriately rated to perform maintenance on the aircraft, that the inoperative instrument or equipment does not constitute a hazard to the aircraft. An aircraft with inoperative instruments or equipment as provided in paragraph (d) of this section is considered to be in a properly altered condition acceptable to the Administrator. So long as each of these provisions are met, the anti-collision light system can be rendered inop and placarded and the aircraft can still be legal to operate.
91.209 (b) (b) Operate an aircraft that is equipped with an anticollision light system, unless it has lighted anticollision lights. However, the anticollision lights need not be lighted when the pilot-in-command determines that, because of operating conditions, it would be in the interest of safety to turn the lights off. Technically based on 91.213 actions above, it is no longer equipped, so this paragraph of the regulation no longer applies
So long as you comply with the above, the aircraft is Airworthy (with regards to the anti collision system) and legal to operate that aircraft.