festus
I did say (twice) to make a note of the entries first !!!
You can easily recreate them manually using the db command if all else fails, and that's why I suggested that approach.
Rebooting the server does very little, except restart services.
Autogeneration only happens when you expand templates & then reboot, which rebuilds the config files based on a combination of the values in the db files and the template fragments.
As you now have wrong (ie no) values in the domains db, then these values will be retained, although in the absence of any keys or properties, default values from the template fragments will be put into the config files.
You need to do
rm /home/e-smith/db/domains
initialize-default-databases
signal-event post-upgrade
reboot
I think that should get default values back, and then you can tailor your domains to set the values you require using the server manager panel.
Configuring settings/values using the server manager panel or the command line, has the same result, except of course for any settings not supported by server manager GUI, which will then require command prompt intervention.