Apologies for the lateness of this.
Comic Vine lists all his appearances, but it's not in any chronological order, and they list books he has appeared in, including redudant references from collected additions. Still...
As mentioned, Duke first appears in the New 52 Batman run. Order should go like this, though be mindful that this isn't 100% chronological either. Some of these apparances doesn't have him do much.
::New 52 Era::
New 52 Batman
#21 - First appearance (as a young kid); Beginning of Zero Year
#30
#33 - End of Zero Year
#35 - Beginning of Endgame; first appearance as his contemporary 16 year-old self
#37-39
New 52 We Are Robin
#1-6 - First appearances in a hero capacity
New 52 Robin War
Comprises a string of issues of ongoing books at the time; a collected addition exists of this story, of which Robin War #1 and #2 (Parts 1 and 6 respectively), Grayson #15 (Part 2), Detective Comics #47 (Part 3), We Are Robin #7 (Part 4), Robin: Son of Batman #7 (Part 5), Gotham Academy #13, Red Hood/Arsenal #7 and Teen Titans #15; note that there are only 6 official parts to the story (the rest are tie-ins) and Duke's role in each, especially in the tie-ins, will vary
New 52 Teen Titans #16 - Though not in the above collection, he apparently appears in this issue, too; don't remember, but it may have been a cameo
New 52 We Are Robin
#8-12 - Takes place after Robin War
New 52 Batman: Superheavy story arc; - Takes place contemporanously to various points of We Are Robin, but the exact timeline is iffy
#42-43
#45-49
#50
New 52 Batman & Robin: Eternal; series takes place at some point post Robin War, but before the end of Superheavy; note that Duke's appearances here are merely camoes -- he speaks few words and isn't really a character in this particular story here; this is more a Harper Row/Blue Bird reading selection, among more classic characters in-focus in the story
#4
#23-24
#26
::Post-Rebirth::
Batman Rebirth One Shot - Duke's first costume is revealed here
Rebirth Batman book; Duke has little role or presence in the stories of this book, as a character or otherwise, particularly after issue 8, the Night of the Monster Men arc's conclusion
#1-8 - #7 and #8 are part of the four alternating issues with Rebirth Detective Comics in the Night of the Monster Men story; they are the first and last parts of the story respectively
#16-18 - Part of the I Am Bane arc; more extended camoes than anything, especially the latter two issues
#33 - Most recent appearance in this book; so far, hasn't shown up again since
Rebirth Detective Comics
#940-942 - The former issue is just a reaction shot cameo alongside Alfred during the issue's climax; the latter two issues are the respective second and third parts of the Night of the Monster Men story arc, alternating with early Rebirth Batman
#952 - A brief cameo where he relays some news, gives some well wishes and goes about his way; so far, hasn't shown up or been referenced since
All-Star Batman; through its first 5 issues and the back-ups, this books had the most consistent in-costume working together of Duke and Bruce of Duke's entire existence; no other book to this point has the characters working together as crime-fighting partners like this one did
#1-9 - Consistently appears throughout the main story of the first 5 issues, with a more subdued role in the 8th and 9th (if I recall correctly); is the main character focus of The Cursed Wheel back-up stories in each of these issues sans the 5th; post Rebirth and prior to the 2 Dark Days prologue issues/Batman and the Signal, this is the most robust and character defining of Duke's contemporary existence, and is a must read for the character; these back-ups will be collected in the Batman and the Signal Trade Paperback
Dark Days: The Forge and Dark Days: The Casting - The two shot-prologue to the Dark Nights Metal story; though Duke has no role in the Metal story proper (outside of Batman: The Merciless, one-shot in which I've no clue of the context of his appearance), he does have a substantial role in the prologue, and events from it are used to lead into the charater's new role in Batman and the Signal
New Talent Showcase 2017
Role Call - A short story written by Batman and the Signal writer Tony Patrick; features Duke in a training session with Red Hood
Batman and The Signal; Duke most recent and contemporary appearance; story focuses on the character as he adopts his new role as The Signal and gains an understanding on his powers; a must-read for the character
#1-3 - #2 is out on the 21st of February (tomorrow); #3 is currently scheduled for April
::Miscellaneous/Non-Canon::
New 52 Detective Comics
#27 - Has a number of short stories, including one with an unnamed, protype of an African Amercian Robin kid, presumably Duke; is from a dream of some kind and is otherwise non-canon (another one features Duke referred to a Lark and Harper as Bluebird, but is also a dream/premonition, and is otherwise non-canon; not sure which issue that was, as it might have been this one)
Batman & Robin: Future's End - A one-shot tie-in for the New 52 Future's End story that acts as a potential future for the characters (Duke as an older Robin with dreads, Alfred, and Bruce); though it makes for a fun read, it's safe to say it's a future that won't come to pass (nor any of the Future's End storylines, aside from Batman Beyond's)
Catwoman: Future's End - Another Future's End "what if?" tie-in focusing on Catwoman; not sure of Duke's role here, as I don't recall reading it
Dark Nights Metal One-Shot - Batman: The Merciless - A one-shot detailing the origins of one of the Evil Batmen characters; I've not yet read it, so I can't gauge Duke's role in it
Rebirth Batman Beyond - Has a wordless flashback cameo, is name dropped, and is otherwise referenced in at least two issues, including #7; issue #16 even shows his current Signal design costume among Bruce's collection in the Batcave; notable for being one of the scant few Rebirth books that acknowledges the character's existence
Rebirth Batman Annual #1 (2017) and #2 (2018) - I have yet to read the second Annual, did read the first; in the first, Duke doesn't have much of a role, and what's there is... kind of insulting
That should be that. This took a while, so I hope this was helpful to you @DragonsChi, and to anyone else looking for Duke Thomas's appearances. Please pardon any typos that may be there. I'll come back and fix them later.