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.
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.