It all depends on weather when you built the automation did you tell the automation to use the local version of the agent, or the remote one. Even then, as long as you don't change the password for the user that is mapping the drives, then you don't need to change or update the agent. The automation is not updated automatically though.
To update the automation, if needed, you will just need to rebuild the automation and push it out to the computers that you want it reinstalled. You will not need to uninstall the old version as all the installs will uninstall the old automation prior to the installation.