You can use the
Lookup file editor app OR
You can deploy apps inside of apps from a Deployer to Search Heads in a Search Head Cluster.
You can deploy apps inside of apps from a Deployment Server to Search Heads and/or Indexers.
You can deploy lookup files with other non-Splunk tools like Puppet, Chef, SCCM, Tanium, etc.
See this (REST API endpoint for managing lookups, see one below this as well for updating individual lookups). You should be able to write a script to do bulk operations using this.