I think this is a bug, when you change the taxonomy in editing custom post type, unexpected meta boxes are disappeared.
here is my solution
// create post object to match against
$post = isset($overrides['post_id']) ? get_post($overrides['post_id']) : false;
+ // fix post_type value
+ $overrides['post_type'] = get_post_type($post);
+
// find all acf objects
$acfs = $this->get_field_groups();