Remember that what you call "splunk server" which in your case is just an "all in one" installation can be deployed as a huge multilayered multisite installation in which you don't have a single component that you could call "splunk server" 🙂 Anyway, the config files have effect in the place they are deployed. So inputs.conf on a splunk component defines what happens on this particular splunk component. There is some additional mechanics involved when you're using deployment server/deployer to manage remote nodes' configuration from a single place but even then you're just preparing a file "locally" and then distribute it to your forwarders, search heads and whatnot and the file gets applied there. But that's not the case as I understand you're not using your splunk server as the deployment server. I suppose you installed your Splunk all-in-one on a Linux box then installed a Universal Forwarder on the Windows server and during the installation pointed it to your Splunk server and checked the "collect windows eventlogs" boxes. After that you installed your TA-windows to the Splunk _server_. So now the situation looks like this: 1) You have your Universal Forwarder with inputs.conf created by the installer during the installation which contains default stanzas enabling event logs collection. Since they haven't been reconfigured in any way they simply pull events from eventlog, set proper sourcetypes and send them to your splunk server which by default places them into the main index. 2) You have your TA-windows installed on the Splunk server and you created inputs.conf there. Splunk is reading this file and probably tries to conform to the settings contained therein but since it's a Linux server it cannot run event log collection because it has no event log to work on (and doesn't have the exe files to perform the process anyway). But still the rest of the TA-windows app is in effect, so your events sent from the Universal Forwarder are properly parsed and displayed when you're doing a search and they're CIM-compliant. If your Splunk server was running on Windows box, the configuration that you created in your hand-made inputs.conf would be applied on this Splunk server and would regard local event log collection (in fact it would be merged with the default settings but that's a topic for another story). In order to force specific destination index and event filtering on input you have to put the inputs.conf settings on the Universal Forwarder that's doing the actual Event Log collection.
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