I am getting error as "Lookup table does not exist. It is referenced by configuration", but i have the lookup on the search head with Global permissions and also it is replicated to indexers( i can see the file on indexer as well). Why it is giving error ?
You need to also set permissions for the Lookup definition. You can do this by going to Settings > Lookups > Lookup definitions. Remember that your permissions for lookup table files must be at the same level or higher than those of the lookup definitions that use those files.
Could you check the permission of the lookup table file, definition(if any) and automatic lookup(if any) for the app you are running the search in?
Sometimes we set the permission at app level and these knowledge objects are not available for use in other apps.