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The mystery of the VX-6 / VXE-6 changing tail codes
First, a little history of the Navy's VX squadrons is in order.
VX = Experimental Squadron 1927-1943.
VX = Experimental and Development Squadron or Operational Development Squadron or Air Operational Development Squadron or Air Development Squadron 1946-1968
VX = Air Test and Evaluation Squadron 1969-present
VXE = Antarctic Development Squadron 1969-1999
VXN = Oceanographic Development Squadron 1969-1993
The original four VX squadrons were under operational control of COMOPDEVFOR (Commander Operational Development  Force).
Today COMOPDEVFOR is known as COMOPTEVFOR and it still controls VX-1, VX-9 and HMX-1.
VX-6 / VXE-6 was not the first Navy squadron to use the tail code of "XD".
"XD" was first assigned to VX-4.
However, it was not the same VX-4 of NAS Point Mugu / Playboy Bunny F-4 fame.
Some web pages on the internet "mistakenly" identify early VX-4 aircraft that have the "XD" tailcode as VX-6 aircraft.
More information about the FIRST VX-4 squadron can be found further down the page.  
Rest assured that VX-6 did not operate any Boeing PB-1W'ss or Martin P4M Mercators!
The Navy has / had the following VX type squadrons assigned:
Air Test and Evaluation Squadron One
Anti-Submarine Warfare 
Patuxent River, MD
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Experimental Squadron Two
Air Development Squadron 2
Drone Controller / Guided Missile Development
Part of Task Group 1.6
TG 1.6 had three different functions: drone plane and drone boat control, aerial photography, and seaplane transportation.
TE (Task Element) 1.6.14 was Air Development Squadron 2 (VX-2)
NAS Chincoteague, VA
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Experimental Squadron Three, also known as Helicopter Development Squadron Three, was established at NAS NewYork 01 July 1946  to study and  evaluate the adaptability of helicopters to Navy requirements.
Besides developing operational procedures and  conducting experiments with helicopters, VX-3 was responsible for training Navy helicopter pilots at the air station. After two years of  increased helicopter activity in the fleet, it became apparent that VX-3 was becoming more involved in fleet operations and less  in development.
On April 1, 1948, VX-3 was disestablished and two new squadrons were established, designated Helicopter Utility Squadrons  HU-1 and HU-2.
Personnel from VX-3 formed the nucleus of the two new squadrons.
Their primary mission was search and rescue,and providing utility services for the fleet. HU-2, based at NAS Lakehurst, N.J., was also tasked with training helicopter pilots and aircrew.
NAS New York
**NOTE** On certain web pages VX-3 has also been listed as being one of the VX squadrons that helped to develop the F-8 Crusader along with being the first navy squadron to operate the Crusader, together with the F4D-1 Skyray and F11F-1 Tiger, from an aircraft carrier deck.
This does not jive with OFFICIAL US Navy sources, and my personal opinon is that they have mixed up VX-2 with VX-3.
VX-4 (Not the Vanguards of Point Mugu)
Established as VP-11F 01 Jul 1936.
VP-11F Redesignated VP-11 01 Oct 1937
VP-11 Redesignated VP-54 01 Jul 1939
VP-54 Redesignated VP-51 01 Jul 1941
VP-51 Redesignated VB-101 01 Mar 1943
VB-101 Redesignated VPB-101 01 Oct 1944
VPB-101 Redesignated VX-4 15 May 1946
VX-4 Redesignated VW-2 18 Jun 1952
For its first land-based airborne early warning aircraft, the Navy in 1945 purchased twenty new B-17Gs and modified each to the  PB-1W configuration by sealing shut its bomb bay, removing the armament, and mounting an APS-20 air search radar in a large   dome beneath the fuselage.
The first PB-1Ws were delivered to VPB-101 in the spring of 1946; the Navy was to purchase a total of thirty-one. The PB-1W  was a delight to fly, being much lighter than the original B-17G, but its lack of cabin pressurization made it cold and uncomfortable for the men operating the radar and tracking systems.
In late 1946 VPB-101 was moved to NAS Quonset Point, Rhode Island, and redesignated Airborne Early Warning Development  Squadron Four (VX-4).
VX-4 moved from NAS Quonset Point, Rhode Island to NAS Patuxent River, Maryland, in July 1948; NAS Patuxent River,  Maryland, as it was commonly known, became the center of Navy airborne early warning for the next seventeen years.
Lessons learned from flying the PB-1W were applied to development of the Lockheed PO-1W (a redesigned Lockheed 749  Constellation airliner later designated WV-1), which first flew in 1949, and to the highly successful Lockheed WV-2 (based on the  famous L-1049G Super Constellation), which was first delivered to the Navy in 1954.
The Navy's "VX" squadrons had the following tailcodes assigned to them:
VX-1 XA / JA
VX-2 XB / JB   
VX-6 XD / JD
From what I can find it seems that in 1957 the Navy's remaining VX squadrons changed tailcodes from "X_" to "J_".
VX-3 and VX-4 had been disestablished by 1957.
VX-4 and VX-5, while being established in 1952 and 1951 were located on the West Coast and were given the tailcodes of XF and XE.
Most of the VX squadrons were located on the east coast.
Now look at the current listing of squadrons that have "J" as the first letter:
VX-1 Tailcode JA 
VR-1 Tailcode JK
VQ-2 Tailcode JQ
VR-48  Tailcode JR  
VR-46  Tailcode JS  
VR-52  Tailcode JT
VR-56  Tailcode JU
VR-58  Tailcode JV 
VR-62  Tailcode JW
You can see how the JD of VX-6 / VXE-6 would fit right in this list had they stayed at NAS Quonset Point.
Even though VXE-6 moved to NAS Point Mugu they kept the "JD" tailcode.
At some point after 1977 they switched (back) to the tailcode of "XD". 
One explination why VXE-6 kept the JD tailcode after the move to Nas Pt Mugu is that VXE-6 migh have still fallen under AIRLANT, and only when VXE-6 was placed into the custody of AIRPAC did the tailcode change to "XD".
If anyone can help fill in the blanks or has any corrections please let me know.