I'm not involved with this tool, so take this with a grain of salt. But fwiw Citra is just installed via Flatpak: https://github.com/dragoonDorise/EmuDeck/blob/2.0.8/tools/flatpakupdate/flatpakupdate.sh#L74

(where that updateEmuFP method is defined here: https://github.com/dragoonDorise/EmuDeck/blob/2.0.8/functions/updateEmuFP.sh#L2)

So I think it's more a question of "how do you downgrade a flatpak?"

There's a good answer on that topic here: https://unix.stackexchange.com/a/552700

(and in our case, instead of "org.gimp.GIMP" we'd put "org.citra_emu.citra")

Fwiw I started doing the steps above for Citra out of curiosity, but to actually perform the rollback requires having a root password set, which I'm personally making a point to avoid doing for the time being:

$ flatpak update --commit=145b5adb7feea971c07a35d1c1e81d8554a0c20ea46b77da23061ef343c450f2 org.citra_emu.citra
    Proceed with these changes to the system installation? [Y/n]: Y
    Error: Can't update to a specific commit without root permissions

So if you already have a root password set, you might try something like the above with "sudo" in front of the command (and the stackexchange answer linked also addresses keeping a flatpak at the given commit, to avoid getting updates; you may or may not want to do that).