My recommendation is that for each project (and I know this is a generalization that all sites can be run the same way)
1) There should only be one project where the Project is driving the Jobsite and all of its Design Content - all other linked projects should have been Linked using Add external Site. When you do this your Project ettings for Field Data should all be set to Protection On - that way a change you make to the Jobsite or Design Data in the Project cannot be sent back out to the field (this is effectively a dissociated project), yet it will allow you to import a copy of the Design Map and Design Surfaces etc that are not linked to the "External Design". You can change those as much as you want and if you want then to send the changed models to the field you can but only as a New Name - the protections will stop you sending out replacement files only New Files for New Designs.
2) When you have everything as (1) when you try to add an External Design, the Protection will stop you from doing this and allow you to import a copy of the Design Data from a controller folder system only - this will be the same as the source data but is just a copy of what is in the controller (TTM for a Surface and Linework from a DXF) - the objects imported are not referenced to the Design at all and so changes will not affect anything.
3) Because your Calibration and Control is protected you will not be able to change that on any controller
4) Because your Site Map is Protected you will not be able to change that either
5) Because your Design Data is protected you cannot change that on any device. You could however Reassign or add assigned controllers to a design when it is referenced into a project
However once you have referenced a Job Site into a Project we do not allow you to remove it as we do not / did not forsee any time that someone would want to reference a single BC-HCE Project to more than one Job Site on SCS900 or GCS900 etc. If you dont want that connection then don't add an External Jobsite and simply drag and drop the data from the Jobsite, Design and Work Order Folders as you need them. If you have referenced an External Jobsite and you want to Protect it, make sure that your Project Settings for Field Data Protection are all enabled, then the data is safe no matter what you do in the project.
Does this answer your question?
Alan