Cowell remained a prisoner for around five months, occupying the time by teaching classes in automotive engineering to fellow inmates. In her biography, she describes the situational sexual behavior shown by some of the camp's Allied prisoners and her discomfort at being propositioned by prisoners who assumed she also wanted to take part in this. She was offered the part of a woman in a camp theatrical production but turned it down, as she thought this would make her appear homosexual in the eyes of other prisoners. Towards the end of the war, food became short at the camp; Cowell lost 50 pounds (23 kg) in weight and later described killing the camp's cats and eating them raw because of hunger.

By April 1945, the advancing Red Army was approaching. The initial German intention was to evacuate the camp, but the prisoners refused to leave. After negotiations between the Senior American Officer and the Kommandant, the Germans guarding Stalag Luft I abandoned it and evacuated towards the west, leaving the prisoners behind. The unguarded and undefended camp was reached by the Red Army on the night of April 30th,  1945. Commonwealth personnel was flown back to the United Kingdom some two weeks later, between 12 and 14 of May, by aircraft of the United States Army Air Forces.

After demobilization, Cowell was engaged in a number of business ventures until, in 1946, she founded a motor-racing team and competed in events across Europe, including the Brighton Speed Trials and the Grand Prix at Rouen-Les-Essarts.

However, her autobiography describes this as a time of great distress. She also experienced traumatic flashbacks when watching the film Mine Own Executioner, in which the hero is shot down by the anti-aircraft fire while flying a Spitfire. 

In 1948, Cowell separated from her wife and, suffering from depression, she sought out a leading Freudian psychiatrist of the time but was unsatisfied by the help he offered. Sessions with a second Freudian psychiatrist, described in her biography only as a Scottish man with a less orthodox approach to his profession, gradually revealed, in her own words, that her "unconscious mind was predominantly female" and the "feminine side of my nature, which all my life I had known of and severely repressed, was very much more fundamental and deep-rooted than I had supposed."

By 1950, Cowell was taking large doses of estrogen but was still living as a man. She had become acquainted with Michael Dillon, a British physician who was the first trans man to get a phalloplasty, after reading his 1946 volume Self: A Study in Endocrinology and Ethics. This work proposed that individuals should have the right to change gender and to have the kind of body they desired. The two developed a close friendship. Dillon subsequently carried out an inguinal orchiectomy on Cowell. Secrecy was necessary for this as the procedure was then illegal in the United Kingdom under so-called "mayhem" laws and no surgeon would agree to perform it openly.

Cowell then presented herself to a private Harley Street gynecologist and was able to obtain from him a document stating she was intersex. This allowed her to have a new birth certificate issued, with her recorded sex changed to female. She had a vaginoplasty on May 15, 1951. The operation was carried out by Sir Harold Gillies, widely considered the father of plastic surgery, with the assistance of American surgeon Ralph Millard. Gillies had operated on Michael Dillon, but vaginoplasty was then an entirely novel procedure, which Gillies had only performed experimentally on a cadaver. The name on her birth certificate was changed on May 17th of that year.

By 1954, her two business ventures, a racing car engineering company (Leacroft of Egham) and a clothing company had both ceased trading, and her change of legal gender had made it impossible for her to continue Grand Prix motor racing. However, in March 1954, news of her gender reassignment broke, gaining public interest around the world. In the United Kingdom, her story was published in the magazine Picture Post, and Cowell received a fee of around £8000 from the magazine (equivalent to £230,000 in 2021, when adjusted for inflation). Cowell's biography was published soon after this, earning a further £1500 (£43,700 in 2021).

In the United States, the widespread sensation caused by the news stories about Christine Jorgensen in 1952 had introduced the American public to the concept of changing sex, and the press had continued to print a steady stream of stories about others who had done so, mostly male to female trans women. Such reports tended to conflate the unrelated concepts of sexual orientation and gender identity, so transsexuality had become closely associated in the public mind with male homosexuality (during this period, highly taboo) and effeminacy amongst men. Cowell's story consequently appeared confusing as it disrupted this narrative. Her marriage, her parenting of children, her wartime combat service, and her association with motor racing were, during this period, perceived as strong markers of heterosexual masculinity; these aspects of her life were described repeatedly in press reports.

She continued to be active in motor racing and attracted some publicity for winning the 1957 Shelsley Walsh Speed Hill Climb. In November 1958, she acquired an ex-RAF de Havilland Mosquito (number TK-655, civil registration G-AOSS). Her intention was to use the aircraft for a record-breaking flight over the South Atlantic. However, the project fell through due to a lack of suitable engines, and in 1958 she became bankrupt with debts totaling £12,580 (approximately £312,700 in 2021). By 1959, G-AOSS was a derelict hulk and its remains were scrapped in 1960.

Her financial difficulties continued, as she found it difficult to get employment. In later years, she largely dropped out of the public eye. However, she was still an active figure in British motor racing in the 1970s. She also continued flying and by this time had logged over 1600 hours as a pilot. 

A brief interview with Sunday Times journalist Michael Bateman appeared in March 1972, when she was working on an (unpublished) second biography. In the interview, she stated she was an intersex individual with the chromosomal abnormality XX male syndrome, and that the condition justified her transition. She also spoke in derogatory terms of those individuals with XY chromosomes who also underwent male to female gender reassignment, saying "The people who have followed me have often been those with male chromosomes, XY. So they've been normal people who've turned themselves into freaks by means of the operation."

In the 1990s, Cowell moved into sheltered accommodation in Hampton, London although she continued to own and drive large, powerful cars. She died on October 11th, 2011. Her funeral was attended by only six people and (on her instructions) was unpublicized – her death was not publicly reported until two years later, when a profile of her was printed in The Independent newspaper in October 2013. The New York Times published Cowell's obituary on 5 June 2020.

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