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robot_upstart can indeed be a helpful package, but due to the issues you encountered I've tended toward making my own systemd service files which gives me full control of how the services are crafted and brought up.

Anyway, to address your question:

To remove a service previously installed with robot_upstart :

$ rosrun robot_upstart uninstall NAME_OF_SERVICE

How to modify the launch file that is tied to that service depends on whether the service was initially created with the 'symbolic' flag, in which case you can modify the launch file at the package level (i.e. in your workspace). If you didn't use the symbolic flag, then the launch file was copied when robot_upstart created the service. This lives in /etc/ros/$ROS_DISTRO/NAME_OF_SERVICE.d/

And just for completeness sake, the service files that robot_upstart creates live in /etc/systemd/system/ and /lib/systemd/system/NAME_OF_SERVICE.service. The commands you can run to start/stop the service are in /usr/sbin/ with the name NAME_OF_SERVICE-{start/stop}

I'm not sure how you want to "modify the configuration of the service" but I interpret that as a combination of modifying the launch file that's brought up and the service file(s) that bring up the launch file. I've never used robot_upstart to make modifications of the service itself, but instead have manually edited the *.service files to do what I want, i.e. bring the service up after networking, adding delays between services, etc.