I had to unsubscribe from CQUI; disabling it was not enough. Details below for the curious.
After the patch, I first tried a game doing nothing (defaulting to a handful of mods), and there were a variety of in-game issues (no surprise). So I disabled all mods, started a new game, and found that clicking on the notification sphere in the lower right did nothing. I don't recall if there were other issues. That wasn't a big deal (e.g., I could open the tech tree on my own to pick a new tech, click on the city to choose production, etc.) until I captured a city and couldn't choose whether to keep or raze. So I couldn't proceed to the next turn.
After reading that some mods required unsubscribing, I unsubscribed from CQUI on steam, loaded the stuck game, and it worked fine - clicking on the sphere brought up the box allowing me to choose whether to keep or raze the city. And since then, the button has worked as it's supposed to for all other actions, too. I'm now well on my way to the luftaballoons achievement with that game (finally having spied the continent of Nena).