HEllo Rob, there is a new version of Calibre web we will be working on soon, that includes the Import manager, meaning you wont have to use the Desktop version of Calibre on the Vps Server.
I think that would serve your needs much better.
here crocodilestick/Calibre-Web-Automated: Calibre-Web but automated and with Calibre features! Fully automate and simplify your eBook set up!
its been discussed here NS8-Calibre-web Application - App - NethServer Community