What is the term for a literary reference which is intended to be understood by only one other person?
I came across this term some years ago but did not record it - wrongly assuming I could easily Google it when needed.
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Unless there's a more specific term that I'm not aware of, you might be thinking of shibboleth:
A shibboleth is any custom or tradition, usually a choice of phrasing or even a single word, that distinguishes one group of people from another. Shibboleths have been used throughout history in many societies as passwords, simple ways of self-identification, signaling loyalty and affinity, maintaining traditional segregation, or protecting from real or perceived threats.
A "furtive shibboleth" is a type of a shibboleth that identifies individuals as being part of a group, not based on their ability to pronounce one or more words, but on their ability to recognize a seemingly innocuous phrase as a secret message.
A literary example:
Mark Twain used an explicit shibboleth to conceal a furtive shibboleth. In The Innocents Abroad he told the Shibboleth story in seemingly "inept and uninteresting" detail. To the initiated, however, the wording revealed that Twain was a freemason.
This isn't exactly what you describe, as it's a reference intended to be understood by a particular group of people, not necessarily just one. But it's close enough that it might be what you're thinking of.
Promoting my comment up, innuendo could work as well.
1a : an oblique allusion : HINT, INSINUATION
especially : a veiled or equivocal reflection on character or reputation
Of note, the d20 system used for the third edition of Dungeons and Dragons used a skill called Innuendo to embed messages meant for a particular target in one's speech or writing.
I think cipher could fit with this.
It depends on how broad your definition of literary reference is. If it's the whole body of text, then the idea is that only someone else who holds the decrypting cipher can decode your message.
a method of transforming a text in order to conceal its meaning
"secret communications written in cipher"