I might be experiencing this issue too, but I am unsure. I am posting
this in case it helps.

After upgrading from Ubuntu 18.04 to 20.04, whenever I remove my
external keyboard and plug it back in, the external keyboard's layout
switches to US English instead of whatever it was set to (a custom
layout in my case, but I confirmed it with other, built-in layouts too).
The laptop's built-in keyboard layout remains correct.

I applied @gunnarhj's fix, but the behavior did not change. (Again, I am
not sure I if the problem I'm experiencing has the same root cause as
the OP's problem.)

However, I was able to work around the problem by switching to Wayland.

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https://bugs.launchpad.net/bugs/1899206

Title:
  Tweaktool Keyboard “Additional Layout Options” not persisting on USB
  keyboard unplug/reconnect

Status in GNOME Shell:
  Unknown
Status in Mutter:
  Unknown
Status in gnome-shell package in Ubuntu:
  Invalid
Status in mutter package in Ubuntu:
  Fix Committed

Bug description:
  I am running Ubuntu 20.04.1 with Gnome. I am seeing new behavior which
  seems to have been introduced within the past couple of weeks. I have
  a couple custom keyboard settings configured in Tweaktool "Additional
  Layout Options". These settings work great.

  I have a USB keyboard plugged into the machine. If I have the keyboard
  plugged in when I start my Gnome session, the customized keyboard
  layout options are correctly applied to the USB keyboard. If I unplug
  and reconnect the keyboard, the keyboard does will _NOT_ have the
  customized keyboard settings.

  If I restart my Gnome session (using Alt-F2 -> "r"), the customized
  settings are applied to the keyboard.

  I think this behavior is something new. Before, I was able to
  unplug/reconnect my keyboard and it would apply my customized keyboard
  settings on reconnect. Is there anything I can do to force the
  application of the custom keyboard tweaks on USB keyboard reconnect?

  Is anyone else able to reproduce this? I don't have any other machines
  with Ubuntu 20.04.1 to test with.

  Thanks!

  (This is also cross-posted at askubuntu:
  https://askubuntu.com/questions/1281162/tweaktool-keyboard-additional-
  layout-options-not-working)

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