I'm running a remote Indi server and I find my current configuration files stored on the server in /home/<user>/.indi
After hitting the "Run" button on Ekos on my workstation, but before I hit "Connect", I saved the config on one device, and looked at the files in the /home/pi/.indi directory and the one I changed had a current timestamp, so it is updating on the server. After I hit "Connect" it updated again, and only the one I changed.
Hope this helps a little.