You have an error in your SQL syntax line 413 of search_api_grouping/includes/datasource_denormalized_entity.inc

Problem/Motivation

We've added a new vocabulary with ~12000 hierarchical terms and got "504 gateway / MySQL server go away" issue.
The full message in Watchdog is :
PDOException: SQLSTATE[42000]: Syntax error or access violation: 1064 You have an error in your SQL syntax; check the manual that corresponds to your MariaDB server version for the right syntax to use near ')) AND (entity_type = 'taxonomy_term') AND( (queued > '0') OR (needs_processi...' at line 2: UPDATE {search_api_denormalized_entity} SET queued=:db_update_placeholder_0, needs_processing=:db_update_placeholder_1 WHERE (index_id = :db_condition_placeholder_0) AND (etid IN ()) AND (entity_type = :db_condition_placeholder_1) AND( (queued > :db_condition_placeholder_2) OR (needs_processing > :db_condition_placeholder_3) ); Array ( [:db_update_placeholder_0] => 0 [:db_update_placeholder_1] => 0 [:db_condition_placeholder_0] => 5 [:db_condition_placeholder_1] => taxonomy_term [:db_condition_placeholder_2] => 0 [:db_condition_placeholder_3] => 0 ) in SearchApiDenormalizedEntityDataSourceController->createPermutationItems() (line 413 of /var/www/html/sites/all/modules/contrib/search_api_grouping/includes/datasource_denormalized_entity.inc)
Happens both in a browser and via Drush cli (drush sapi-gg, etc). It is 16G RAM Fedora workstation with pretty much resources dedicated to MySQL. Please advise.