In 3.0 you can cut and paste the output folder to your htaccess folder, and 3.0 would create a new output folder next time opening project. In 3.1, if the output folder is missing, it crashes on build project.
Jim, Project is a not only one file in new PHPRunner 3.1.
Each project now resides in it's own folder and include a set of template files, output directory, virtual directory etc. Simple renaming or copying a project file is not enough. Copying project folder to another folder along with renaming project will do the job.
Besides that you need to change output directory accordingly and create a new virtual directory that points to the new output directory.