I don't believe it's a change in a splunk .conf file. When you run the CLI that several people mentioned below, it will make an entry into /etc/init.d I believe. That's where you'd have to check, but you can't roll something out via the deployment server to that location.
You may want to write a script that takes a list of hosts and runs the CLI on each host.
Hello, I know there is a CLI command for it but we forgot to do this on a couple UF and would like to do a mass config change. We are just looking for a particular flag in a .conf file to set and push out.