[6] His reputation was damaged in 2011 when he made – and subsequently recanted – a written confession that he had tampered with a document signed by President Abraham Lincoln held in the U.S. National Archives.

[15] After retiring from a four-decade career in medicine, Lowry – assisted by a new wife, Beverly – shifted in the 1990s to writing non-fiction historical works.

[16][17] Lowry's first and best-known book on this subject, The Story the Soldiers Wouldn't Tell (1994), received a favorable review in The New York Times as "the first study of sexual behavior associated with the Civil War,"[18] and was praised in Esquire as "amusing and fascinating.

It was alleged that Lowry's motive was to gain publicity by claiming that he, as an independent researcher, had found what would have been the final official document signed by President Lincoln before his death.

[25][26] Lowry subsequently recanted his confession, in which he detailed how he used a fountain pen containing fade-proof, pigment-based ink to alter the date of the pardon.

He maintained that he signed the confession under duress after accepting a request to be interviewed by two NARA investigators at his home in Woodville, Virginia,[27] and that any document-tampering was carried out by an unknown party prior to Lowry citing the pardon.