When editing a post type using MB AIO, I set a custom slug and save it. It seems to save to the database. But on reload, it pre-fills the value of the singular post name.
So if I edit something else on the CPT, and forget to put my custom slug, it will set the wrong slug, and effectively disable the taxonomy until I fix it.
The option Custom rewrite slug in Meta Box > Taxonomies > Edit/create a taxonomy > Advanced still works as well after Save the Permalinks again.
Rewrite slug means to change the default taxonomy slug with your custom slug in the Permalink. Could you please share some screenshots if the problem still persists?
This should be a fix / feature deployed... your answer doesnt suggest it's an issue of metabox, but instead a user should know to do this - CPTUI offers to do this, and this is super basic feature and shocked it's omitted from metabox.