You are correct. When you publish an app from one environment to another they will have different GUIDs. So any connection that you had in NPrinting on one system will not work with the other.
Working with NPrinting in multiple environments has been a huge challenge. Currently we only have a single NPrinting instance. Not ideal as we are basically developing in Production. Since we have not setup a 2nd instance of NPrinting I have not had the opportunity to try to figure this out yet. My guess is that it is not easy currently.
Hopefully someone else has already lived through this.