Support › MB Custom Taxonomy › Rename Taxonomy
If I rename a taxonomy with it's slug, all the items under that taxonomy are deleted.
What is the proper way to rename a taxonomy in Meta Box?
It's the default behavior of the plugin and WordPress. Taxonomies are differentiated by slugs. So you should never change their slugs.
If you have to change, please go to phpMyAdmin and change the taxonomy in the table wp_terms. This is the only way I know.