Hello Brian,
I understand your initial question because I've wondered about it myself. I think it's because, unlike other software, all the imports and edits are "saved" as you work. In PDR, Microsoft Word and dozens of other programs, we're prompted to "Save" before closing.
So, yes, when you want to start a new project in PhD it needs to restart. The above is the only reason I can think of for that.
On your other question, each new project has its own folder & that folder can be stored wherever you wish. Though I don't necessarily have a separate folder for each "shoot", most of my PhD projects are stored in Documents/PhD Projects.
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