@Adaolin Okay, so the funny thing is that when I activate or deactivate transparency it changes correctly.

So this is pre switching
2023-07-30 21_46_22-This PC.png

This is when it switches due to "Use dark mode at sunset"
2023-07-30 21_48_28-This PC.png

And this is after toggling the transparency effect
2023-07-30 21_48_56-This PC.png

It seems like f.lux just does not force a reset or something?
Because the transparency does make the explorer window flicker once and resets the look.
Also, the way that it looks in the second picture does not take effect until I close the window and reopen a new instance.