As always, "it depends".
If the existing inputs.conf is located in
etc/system/local/ (or worse,
etc/system/default/), you cannot modify it via Deployment server, because DS only deploys to the
etc/apps/ directory. (besides some rather ugly hacks using scripted inputs)
If you however have an inputs.conf in an app, you can simply recreate that app on the DS in
etc/deployment-apps/yourapp and then distribute it to the forwarders (assuming you configured the DS IP/hostname with those forwarders).
Be aware that you need to recreate the whole app before distributing it via DS, because all files in that app that only exist on the Forwarder, but not the DS will be removed.
Hope that helps - if it does I'd be happy if you would upvote/accept this answer, so others could profit from it. 🙂