When timeline/assignment/durations need to be changed, we typically put it back into a 'non-active' status. We do this to avoid assignees from getting multiple email notifications as things are adjusted. Then we move it back into active when done. However, they do get an email stating the project is 'active' and it is confusing people because they already received that email when it went 'active' the first time. I searched and found a question that was posted a couple of years ago (see link below) but I didn't really see a response that addresses my situation.
I've not tested this, and suspect you'd need to think through the list of Side Effects May Include, but if you were to create and use a new Project Status called "Re-Activated" (based on CUR, for Current, which I presume you've renamed as Active), because it is not then the built in CUR, might not send the emails that are causing confusion.