I'm assuming you are using deployment apps and serving them with the deployment server to the deployment client (forwarder). If so, take a look on the forwarder for the deployment app(s), and verify they are what you expect.
Say, for example, that the deployment app that you are storing the input.conf files (listed in your question) is called MyDeploymentApp (and it is in $SPLUNK_HOME/etc/deployment-apps on the deployment server/indexer). Take a look in $SPLUNK_HOME/etc/apps on the forwarder and you should see a MyDeploymentApp directory (or whatever your deployment app is actually called). If so, look in the default subdirectory at inputs.conf and make sure what is there is what you expect to be there (that is, the input.conf file on the deployment server). If it is there, make sure that as user splunk you can access the files on that forwarder you are trying to monitor. If it is not there, then grep for the IP address of the forwarder in the splunkd.log file on the deployment server and look for any trouble there. Also, make sure that the deployment app name is associated with a serverClass in the deployment server's $SPLUNK_HOME/etc/system/local/serverclass.conf, and that the forwarder's host name is associated with the serverClass as well.
You should be making changes to the serverclass.conf file using forwarder management so it will be also in the live configuration. If you are doing them manually then you'll need to restart splunkd if you make new changes.
You should also be able to see the deployment app bundle on the deployment server in $SPLUNK_HOME/var/run/tmp/MyserverClass (or whatever your serverClass is called) directory as a .bundle file. This is a tar file created by the deployment server when these conditions exist on the deployment server:
The serverClass is declared in ~/etc/system/local/serverclass.conf
The deploymentApp is associated with the serverClass in ~/etc/system/local/serverclass.conf
The deploymentApp directory exists in ~/etc/deployment-apps and is properly populated
The serverclass.conf file is in the live configuration
Whenever you make changes to the deploymentApp, they should be sent to the forwarder in due time, but you can push it up a bit using splunk reload deploy-server -class MyserverClass (or whatever your serverClass is called).
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