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I'm having a sort of similar issue to this.I get the same problem. I want to run two monitors at different refresh rates but if I turn one off for any reason and then back on, Windows forgets my setting and goes to the setting on the monitor that was on all the time. The only solution for me is to run both monitors at the same refresh rate. Fortunately they can do that.
I've got my new 4090 FE connected to the same 4 screens my old GTX1080 was running. One of those is an old-ish 1440p BenQ screen. It worked fine with my old Win 10 PC but for some reason on Win 11 it needs to be set to 59Hz to not have a weird intermittent flicker at the top left of the screen. Annoyingly though it seems Win 11 resets the screen every time the PC turns on back to 60Hz, which the display considers it's optimum rate.
Going to need to find a way to get it to not do that as that will get old real quick.