The .PJS file for my Suite has disappeared. Is there a way to restore/create another?

Doing a "Save As" of the PJS file will simply move JUST the PJS file to a different folder.  The rest of the associated files will stay where they are, as far as I know.

Best practice for retaining automation projects is to implement a source control tool of some sort (GIT, Mercurial, TFS, etc).  That way, if you want to move a project to a different folder, you simply do a "get" of the project in the new folder (or clone the respository, etc).  This also has the bonus of keeping a backup of all your files right at your fingertips.  Test Automation IS code, it is software development (of a sort) so any best practices that are followed in an application development environment should be followed for test automation development.

If you don't want to do that, then the best way of moving an entire suite is to do a full copy of files, folders, and subfolders to a new location.  This still runs the risk of there being some associated files that may not be in the direct path of the suite so you'll need to be aware of that.