I found Yen in the other tower over the kitchen, after that quest started and everything is alright. There is no mark on the map, but only thing is that you need to go to this second tower.
Thank you for this post.
The solution to the problem is so weird. Visit the other towers and as Mikkil says there will be no mark on the map, but for some reason doing this did cause Yen to spawn where she's supposed to be. This makes no sense to me but it worked.
I have watched the quest on YouTube more than once. I definitely went to the correct tower several times.
I even sent an email to "tech support" at CD Projekt Red maybe a week ago. No one has responded. I expected better from CDPR but here we are. Lesson learned. Also GOG's money back guarantee? Don't count on it! This is what happens when you try to actually use it. Radio silence. Maybe I'll actually get a response once the 30 days is up? Hah I guess we'll see if that happens.
Thanks again Mikkil!
The quest is still a little bugged but it's not a big deal. Here is what you may expect to experience but it does not cause problems:
* The explosion happens as you go up the stairs but Yennefer is not in the room.
Solution: Don't worry. Walk into the room anyway and the cutscene and conversation will begin despite the fact that Yennefer is still not present.
* There are two Yennfers in the cutscene.
It's weird, but it's nothing to worry about. You will interact with one of the two Yennfers and the other will do whatever it does. In my cutscene she just kep leaning over as though to look at the megascope, would stand back up, lean back over to look... and didn't stop the entire time. However, the cutscene works, the quest (and your game!) continues and nothing else odd is caused by this weirdness.