Are there any references in XCOM 2 as to what happened to Dr. Vahlen? Dr. Vahlen was the Chief Scientist who had Tygan's now current role, but she is no longer seen at all, and I can't find any reference in-game referencing her, or any voice comms talking about her, despite the wiki saying that they talk about her being missing.
She's mentioned in the XCOM Archives in the Commander's quarters (bold emphasis mine):
Many of the characters will also mention her from time to time in the Avenger:
I have my suspicions that Vahlen was actually captured by the aliens and used as the basis for the Codex unit, but that's pure speculation at this point.
Vahlen is mentioned in the prequel novel. Minor spoilers follow.
The prequel novel, in the large, deals with the Resistance's efforts to find and capture the crashed alien vessel which becomes the Avenger.
Early on in the novel, the protagonist and his squad travel via submarine to a volcanic island off the coast of South America. That island contains a hidden Resistance research base known as 'Wunderland', which is headed by Dr. Vahlen.
Unfortunately, one of the protagonist's friends has some sort of tracker embedded in her, and ADVENT forces attack the island. The protagonist's squad heads to the surface to fend off the enemy forces. While they're doing so, the base self-destructs.
By the time they've fought off the ADVENT troops the submarine's departed. They explore the now-wrecked base and discover a diversion - a bunch of wrecked helicopters and dead bodies intended to fool any ADVENT forces looking for survivors. A trap door leads to a cove where the protagonist's squad commandeer a boat to continue their journey.
Vahlen's fate is left unmentioned, although the protagonists theorize that she and whoever survived the assault fled on boats (or even a second submarine) after self-destructing the base.
In short — if the prequel novel is considered canon, Vahlen was alive, well, and conducting research for the Resistance weeks or (at most) months before the actual start of the game, but her current whereabouts are still unknown. She may have died escaping her base, been captured by ADVENT while/after escaping, or slipped away and made it to another Resistance haven.
Central mentions her from time to time when you hang around in the avenger long enough. Quotes I've personally heard are
"broken transmissions in what could be German have been broadcast lately"
"Dr valhen is missing but I need to believe she's still out there somewhere"
"valhen went missing after xcom fell but I can't imagine she would just give up so easily, not with earth's freedom at stake"
There's another reference to her in the game: If you play the tutorial, when you're waking up after having the implant removed and Bradford talks of losing good soldiers, you see a photo of Bradford, Shen and Vahlen at the time of EA/EW.
WHAT FOLLOWS BELOW THIS, IS INFORMATION THAT CAN BE QUALIFIED AS SPOILERS. DO NOT READ IF YOU DO NOT INTEND TO SPOIL THE STORY FOR YOURSELF!