We’ve found a solution by deleting a .sock file for the user:
rm /var/run/ondemand-nginx/johndoe/passenger.sock
and then restarting the pun:
sudo nginx_stage pun --user 'johndoe' --app-init-url 'https://myportal.edu/nginx/init?redir=%2Fpun%2Fsys%2Fdashboard%2F'
It may have been that killing the process using the Unix kill command did not also remove the .sock file. The error the user was seeing was “Service Unavailable” when accessing the portal page. The following error message displayed when the user tried accessing the dashboard URL https://myportal.edu/nginx/init?redir=%2Fpun%2Fsys%2Fdashboard
Error -- nginx: [alert] kill(34321, 15) failed (3: No such process)