Context Loss Leads to Unplayable Warhammer 40K Mechanicus?

I’m playing Warhammer 40K: Mechanicus (Warhammer 40k: Mechanicus - Opening Scene - YouTube)

But any loss of window context (the game is fullscreen) causes certain UI elements to become unresponsive. Any interruption causes this (a window prompt opening and the focus switching to it, using the super key, etc).

Is there any way to force context on the game to avoid this from happening?

I’ve lit the incense, but it appears to be ineffective so far. I think a more technical solution is needed to calm the game’s machine spirit.