The “Keep settings” checkbox is a more advanced feature.
If you do not precisely understand the button's use cases, uncheck “Keep Settings” every time you flash a new LEDE sysupgrade to your device, to not preserve settings.
/etc/sysupgrade.conffile that is read by sysupgrade when it is backing up files. Click “Submit” when done editing.
Despite the warnings on this page, keeping settings in sysupgrade works for most of times.