Deleting an Upstart.conf file without stopping software run by service.

Hi,

I have a rapid deployment set up that I use upstart for. I use Upstart on Ubuntu 14.04 to keep programs running, but during each subsequent deployment, I set the current program to unavailable, and deploy the new one. This allows users to take their time and then the software ends automatically after all the users have logged off.

Right now I'm deleting the .conf & .pid with the newest deployments, and usually(90%) this works, but sometimes the older version is unallowed by upstart to exit and I have to manually go back and say stop servicename, and I get this:
stop: Method "Get" with signature "ss" on interface "org.freedesktop.DBus.Properties" doesn't exist.

Is there a reliable or expected method to delete a .conf and unload the service from memory without stopping the software run by the service? I'd appreciate any thoughts, I've been through the upstart manual and tried a lot of things over the past couple weeks.

Thanks,
Damion