you should avoid any manual modification directly on indexers
To modify a setting, you need to push it via the cluster master so it's consistent between cluster nodes.
the cluster master server.conf define the cluster master settings, not what's pushed.
What's pushed will be under etc/master-apps
in it you have 2 choices :
1) go in _cluster/local -> create a server.conf here and use this setting
2) create a configuration app with the file in it.
(btw you should already have put your TA here as they may contain index time configuration)
(go with choice 1 if you don't know how to create a configuration app)
then run on the cluster master splunk apply cluster-bundle
the cluster master will initiate a rolling restart if necessary