AEM Linked folder and document folders in a project template behavior in a sandbox refresh and package promotion

For sandbox refreshes: We noticed the refresh resets the AEM Workflow config in the project templates. This means we have to manually configure it after each refresh. We'd appreciate it if this workflow would remain unchanged for the project templates because we use it for the AEM linked folders upon project creation. 
Second, for the environment package promotions: When we promote a project template there is no way to promote the document folders within it. This is another manual configuration we must do every time for each project template. 

It would be very helpful if these would not reset or if there was a way to edit multiple project templates all at once.