I'm not sure what happens if you try to send a forwarder two copies of the same app. One would probably win over the other, and you wouldn't have your desired result.
What you want to do is leverage Splunk's built in configuration-merging functionality. If you need to send a few lines to one server, just make a new app with those few lines on it! Splunk will automatically merge the apps together into its running configuration.
For example, most apps ship with inputs disabled. You can send out the unix app, and it won't collect anything. But to certain servers, you can also send an app that has just a local/inputs.conf of
[script://./bin/vmstat.sh]
disabled = 0
As long as your setting is in local/ , it will always override the settings in the unix app's default/ - no matter what your app is named.
To check merged settings, run bin/splunk cmd btool <name of config file> list and --debug will list down the list which app the particular setting came from. For example, bin/splunk cmd btool inputs list --debug
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