Manually editing the pushPullSetup.xml file will invalidate that file and the EMS will move the modified file out of the way and start with a fresh config file. Removing the pushPullSetup.xml file is actually a good way of starting the server fresh (without any existing pushes and pulls).
The best way to remove a config, though, is to issue the removeConfig or shutdownStream commands. You need to lookup the id of the stream with the listStreams command, or store the id when you get the reply from your initial command.
Issuing the pushStream command will result in multiple targets if you do not also issue a removeConfig or shutdownStream command.