The real question is: How can a nodeRED installation on a computer (e.g. RPI) be used in a way that a running project can be executed and on the other hand further work on other projects can be done.
See on page: Projects : Node-RED
Open an existing project
Node-RED only runs one project at any time. By opening another project you change what flows are running.
This is probably not the separation that is desired here.
See also Deploy a nodeRED project