I feel your pain, the deployer will throw EVERYTHING in default ( ie. not editable ) . I have had some success at fixing config problems with finding the captain, editing the file, reloading ( NOT reboot or you loose the captain - debug refresh ) the captain, and force syncing all members to the captain. UGLY.
I think the best bet at this stage of search head cluster maturity is to make the rest API your friend and use the config file calls that allow updates to elements, stanzas, or the whole thing. These would be "legal" synced by raft calls to the cluster.
I'm sure it will get better with time, 6.6 just added a fix for ownership that used to kill us when someone left and their ID was no longer available ( yet they owned popular knowledge objects )
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