How to stop a second Studio package overwriting existing project settings

I receive a package from an agency, open and install it in Studio 2017, then I add my own TMs, TBs, and my own QA settings, etc. and complete the work.

A few days later the agency sends me another package for the same client. This second package is created from the SAME agency project. When I open the package Studio automatically installs it in the same project on my computer, OVERWRITING all my project settings, as above. So I have to configure them again. 

I know - I use Project Templates, so it takes a bit less time than asking this question. But is there a way to STOP this behaviour? I haven't found it yet.

 

Thank, Simon