I am experiencing this as well, it worked on 20.04 Focal and is broken
on 20.10 Groovy and 21.04 Hirsute as of today with the latest Hirsute
packages.

I am using GNOME with a Logitech T650 touchpad. If I unplug and replug
the receiver it forgets again. I then have to toggle both natural
scrolling (Settings->Touchpad) and "mouse click emulations" (Tweaks)
each to have it work again.

Given this is apparently common accross GNOME and KDE perhaps it is
somehow related to libinput rather than gnome-shell/settings/etc?

** Also affects: libinput (Ubuntu)
   Importance: Undecided
       Status: New

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https://bugs.launchpad.net/bugs/1902351

Title:
  forgets touchpad settings

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