Only two of the gems' locations are in the adventure
The opening of chapter 12 (p. 173) describes that each gem was taken.
Ten years ago, one of the vineyard's gems was dug up and stolen ... No one knows what happened to the gem.
... the wereravens have been fending off attacks by Baba Lysaga's scarecrow constructs. Three weeks ago, during one such attack, another gem was found, dug up, and taken. Davian believes that it is in the possession of Baba Lysaga ... Davian's belief is correct ...
Five days ago, evil druids stole the third and final gem and bore it to Yester Hill ...
So, we know that the second is with Baba Lysaga (confirmed on p. 163 and p. 166 when describing her hut) and that the most recent was taken to Yester Hill.
On p. 198, it reveals the location of the most recently stolen gem:
Planted in the "heart" of this wooden effigy is a magic gem stolen from the Wizard of Wines vineyard
There's also a special event (on p. 200) called "Druid's Ritual" that describes the druids awakening this wooden statue to summon a tree blight to attack the winery. Also on p. 180, the special event "Wintersplinter Attacks", which is this same tree blight attacking the winery.
How I resolved it
The gem in Wintersplinter and the gem in the wooden statue is the same gem, but in my game I had it be two separate gems. Since I ran the latter special event, the party did not witness Wintersplinter's creation, so the gem used to power that tree blight was the latest lost gem, but when they went to Yester Hill after that, I had the statue be still intact, containing the 10 years ago gem. Wintersplinter was just an awakened tree in my run of this, rather than being related to that statue.
For all three gems to be part of the adventure, you would need to improvise and adjust some details like I did, or otherwise add it to the world yourself. It's up to the DM.