"I will tell you in a few words; but, before I begin, let me caution you that this is an affair demanding the greatest secrecy, and that I should most probably lose the position I now hold were it known that I confided it to anyone." (17)
As we soon learn, it's secret because the royal lady has a secret she doesn't want the royal man (or the public) to know about. By concealing the details of this from the reader, the narrator too is practicing deception—deception by omission.
"During its perusal she was suddenly interrupted by the entrance of the other exalted personage from whom especially it was her wish to conceal it." (28)
In most mysteries, the goal is to reveal a secret that's been concealed. Here, the goal is to keep the royal lady's secret from being revealed, by revealing the secret location of the letter, which was purloined from her. What a tangled web of deceit!
"To be sure, it was to all appearance radically different from the one of which the Prefect had read us so minute a description." (115)
But…but we thought you said it wasn't hidden at all? The point Dupin seems to be making is that even the best disguise leaves a hint of the person (or letter) underneath it. No deceit can be entirely effective.
"In the meantime I stepped to the card-rack, took the letter, put it in my pocket, and replaced it by a facsimile (so far as regards externals), which I had carefully prepared at my lodgings—imitating the D— cipher very readily by means of a seal formed of bread." (117)
Interesting vocab choice, Poe. A "cipher" usually refers to a written code, or, the key to a written code, but it can also mean "a combination of symbolic letters; especially: the interwoven initials of a name." Here, it probably means both. It literally means the D— seal Dupin created for his fake copy of the disguised letter, and it also symbolically stands for the seal when Dupin uses the fake. But what's the difference between the real and the facsimile?
"The pretended lunatic was a man in my own pay." (118)
Here's another layer of deceit: in order to purloin the letter from D—, Dupin stages a deception. He hires a guy to shoot a gun with blanks out on the street so that D— will go to the window, allowing Dupin to purloin the letter. In addition to deceiving D—, Dupin is deceiving the public—both in continuing to cover up the royal lady's secret and in hiring a "pretended lunatic." (And you have to wonder what's going to happen to the "pretended lunatic.")
"But what purpose had you," I asked, "in replacing the letter by a facsimile? Would it not have been better at the first visit to have seized it openly, and departed?" (119)
It's not enough for Dupin to just get the letter back. He's got to play along with this little game of lies and deceits, and so we have to ask: if their positions were reversed, would D— and Dupin act any differently?