Whats the exact line you got in your admin.template file?
Should look something like this one:
<option value="', $option[0], '"', (!empty($config_var['value']) && ($option[0] == $config_var['value'] || (!empty($config_var['multiple']) && in_array($option[0], $config_var['value']))) ? ' selected' : ''), '>', $option[1], '</option>';
Yes, the settings will still be there, I rarely offer an option to delete them unless I build my own tables.