Resolution:
You do not need to restart the BC engine when changing Partner and BusinessAgreement settings. Also, you don't need to restart BC even if you update a file reference in the Partner or BusinessAgreement settings.  The only time you will have to restart BC is a file reference is used in the Operation Editor and you change an .ecs or schema file's content without changing the file reference in BC (this does not apply if you us an uploaded file in the Operation Editor).