If you list a few key points or issues to read-I don't think you can alienate those folks.
If everything somewhat counts-
Huntress
1st appearance
Maybe the last 3 issues of her first solo teaming with Batman
Showcase 93 short story
Contagion issue where she dressed as Batgirl
Joining JLA
It's not the job of the Bat Office to wait on others to figure out what is cannon or not. If someone wants to get mad-tell them should have did it before I did.
I think it is natural result of "everything happened" premise that we got after Dark Death Whatever Metal. Once they'll start putting down on paper actual facts like origin story or key moments in character's history then entire premise is going to crumble so better pretend that everything is fine.
So it looks like there's no Secret Files issue being solicited for December. It'll be interesting to see if they're done with them post Fear State/Tynion, or if they're just taking a break.
Outside of the first two, the rest have all been focused on Tynion's OCs. I'd really like to see them do a few more on existing characters that don't currently have a solo- Tim seems to be MIA at the moment post-Urban Legends 10, Kate Kane could get one, Azrael, even use one to better introduce Ryan Wilder into continuity besides her two appearances so far.
A Jim Gordon issue without The Joker and not written by Tynion would be my wish!
I guess it really depends on how Williamson approaches being the head of the line now.