Have a cloneable group field, add one, delete that one, and then add a new. Then all the taxonomy radio fields in that group field take the last option. Not an issue before deleting to 0 and then adding a new. Can you replicate?
[
'name' => __( 'Example', 'your-text-domain' ),
'id' => $prefix . 'example',
'type' => 'group',
'sort_clone' => true,
'clone' => true,
'max_clone' => 5,
'class' => 'repeatable-section',
'add_button' => __( 'Add new', 'your-text-domain' ),
'tab' => 'page_6',
'collapsible' => true,
'clone_empty_start' => true,
'default_state' => 'expanded',
'group_title' => '{#}. Paper',
'fields' => [
[
'name' => __( 'Example taxonomy', 'your-text-domain' ),
'id' => $prefix . 'Example taxonomy',
'type' => 'taxonomy_advanced',
'taxonomy' => ['type-of-research'],
'placeholder' => __( 'Select option..', 'your-text-domain' ),
'field_type' => 'radio',
'columns' => 12,
],
]
.
