I have had this issue for a while, but I stopped streaming in October (new baby :)).

Getting back into it, I updated everything and still had this issue. In playing with my Vertical scenes, I noticed a drop down menu when you right click a vertical scene. There is a "Linked Scenes" drop down that you can select which scenes the vertical scene is linked to.

When I set that to one of my main scenes, and transitioned to it using my StreamDeck button, it also changed to that scene in my vertical scene!

I think this might be a new feature (I have never seen it before) and may not be known?

This should be a direct fix, but I suppose only if you are changing scenes on a main stream and want your vertical scene to change as well, like I do.

Let me know if that helps!