The Project Settings are stored in the DGN so in your case when you open a new one the Project Settings are empty. You can remedy this by creating a DGNLIB where you set the Project Settings as you want and then add that DGNLIB's path to the MS_DGNLIBLIST config variable and also add or append the following civil variable, CIVIL_CONTENTMANAGEMENTDGNLIBLIST, with the full path to the DGNLIB file.
communities.bentley.com/.../7057.video-multiple-survey-settings
communities.bentley.com/.../7058.transitioning-to-bentley-civil-survey-document
communities.bentley.com/.../7057.video-multiple-survey-settings
communities.bentley.com/.../7058.transitioning-to-bentley-civil-survey-document