We recently had two projects deleted by a user (we can't track who, though, and Bluebeam couldn't tell us). This has happened to me one other time, so we try to warn our users during our training sessions.
I believe the user meant to "Remove From List" but instead chose "Delete" not realizing it would delete the entire project.
Perhaps "Deleting" the project could be a separate "Applied Permission" level? The "owner" of the project is required to give permission to restore a deleted project, but anyone can delete the project? Seems backward.