[Answer]-Running the rebuild_index command more than once looks like it tokenizes values again

This happens because instance variables in the backend need to be reset before running rebuild_index a second time.

from django.core import management
from haystack import connections
backend = connections['default'].get_backend()
backend.setup_complete = False
backend.existing_mapping = None
management.call_command('rebuild_index', interactive=False, verbosity=0)