The 1966 Defence White Paper that cancelled CVA-01 also authorised the major modification of Ark Royal to operate Phantoms. It came out of that refit in 1970 and was withdrawn from service in 1978, which is quite a poor return of investment by anybody's standards. Once the decision had been taken to abandon fleet carriers, it would have seemed logical to scrap the whole idea of sending the F-4 to sea, and withdraw the carriers as they became due for maintenance.
Was there any particular reason why the Wilson government invested so heavily in a capability that it had already decide to abandon? My suspicion is it that was just to ease the pain for the RN, rather than to counter an identified threat.