I'm having very similar problems with my game. To answer the inevitable question of "Well is it a late-game with lots of units?" I say I've been experiencing this from 1.31.1 all the way to 1.31.3 where the fps drops to ridiculously low numbers. Normally my game runs 60 fps or higher, but after the new updates, I'm usually running somewhere below 40 for a "good" experience. When it gets really bad it hits 10fps or even lower and just stays there. It doesn't matter what I'm doing, If I scroll out all the way, stop moving a unit, or anything. I turned some graphics settings off and it continued. I also have tried restarting many times, which occasionally will give me a temporary fix where it goes back to 40 or so which is bearable.
However, I'm extremely displeased with how the game is running recently and I can't even really get a good game in whether it be single-player or multiplayer. I'd really appreciate some performance changes, but I doubt it will happen on PDX's end. They barely fix bugs for years and even said it themselves the plan was to push out content and then fix bugs later. This is a poor game design model on top of the need for a newer engine on their newer games. I just hope at this point eu4 gets a bit more of a performance, bugs, stability, and multiplayer update rather than another DLC because that is what it needs.
If anyone does have even a slight solution to the fps problems I would appreciate that a lot.
