I have the same issue addressed for D7 here: Bulk Generating URL aliases for taxonomy terms doesn't do anything or here: Bulk update for unchecked "Generate automatic URL alias"
And I'm looking for a corresponding workaround for D8, querying the DB directly.
For D7 seems that the following solution works:
UPDATE pathauto_state SET pathauto="1" WHERE entity_type="taxonomy_term";
I did some research for D8:
- cannot find any "pathauto_state" table within a D8 database
- so I tried to find how and where the “Generate automatic URL alias” is stored but without success (see also for this: Where is the "Generate automatic URL alias" setting stored?)