I think it would be helpful to have a new interface when bulk publishing that allows a user to select which layers should be published, unpublished, or synced. When setting up bulk publishing have an interface that shows all the datasets available through the database connection with three different options associated with each dataset depending on its status. One option for publishing, another for unpublishing, and a third for syncing. Then have a way to select multiple datasets plus a select all/unselect all button. That way users can manage the datasets in bulk or individually as is needed.
I have found that initially the publish everything available to the database connection is great, but after that I need to make small adjustments to individual layers over time and not everything all at once.