If your HomeRunner Toolkit module settings are cleared and your modules show as off after an update, the update itself is not the cause. A normal plugin update does not change settings.
Why this happens. WordPress lists any spare copy of the Toolkit plugin folder as its own inactive plugin on the Plugins screen. Deleting that inactive duplicate copy runs the plugin’s uninstall cleanup, which removes the shared settings that the live copy uses.
What changed. From Toolkit 3.286.1 onward, the uninstall cleanup skips itself when another copy of the Toolkit is active, so deleting a spare copy no longer clears your settings.