A bug was discovered in Drupal 8.6.0 that can lead to taxonomy data loss during the upgrade. For this reason, anyone upgrading from previous versions of Drupal (8.5.x) should directly upgrade to 8.6.1 instead of using 8.6.0.
For more information:
- Drupal release notes for 8.6.1
- D.O Issue 2997960: Missing taxonomy hierarchy items in 8.6.0 after running taxonomy_update_8502