Check if an entity has been flagged:
/**@var \Drupal\flag\FlagService $flag_service */
$flag_service = \Drupal::service('flag');
$flag = $flag_service->getFlagById($flag_id);
return $flag->isFlagged($node);
Get all flagging users for an entity and flag:
$flagging = $flag_service->getFlaggingUsers($entity, $flag); // $flag is optional
Flag an entity:
$flag_service->flag($flag, $entity, $account); // $account is optional
Unflag an entity:
$flag_service->unflag($flag, $entity, $account); // $account is optional