Had to split a repeatable section from an ACF post, to it's own post, and then use Posts 2 Posts plugin to preserve the relationship. This managed to keep all the meta data intact for ACF to pick it up (as long as the fields in the new group had the same name) Top level repeater was 'brands' under a post in the advertisers cpt.

sub-repeater-acf-migration.php

$args = array(
   'post_status' => array( 'pending', 'draft', 'publish' ),
	'posts_per_page' => -1,
	'post_type' => 'advertisers'
 );
 
 $query = new WP_Query( $args );
 
 while( $query->have_posts() ) { 


 	
 	$query->the_post();

 	the_title();
 	 	
 	$num_brands = get_post_meta( $post->ID, 'brands' , true );

 	$advertiser_id = $post->ID; 
	
	$post_meta = get_post_meta( $post->ID );

 	$count = 0;

 	while( $num_brands > $count )
 	{
		$new_post = array(
							  'post_title'    	=> $post_meta[ 'brands_'.$count.'_brand-name' ][0],
							  'post_content'  	=> '',
							  'post_status'   	=> 'publish',
							  'post_author'   	=> 1,
							  'post_type'		=> 'brands'
							);
							
		$pid = wp_insert_post( $new_post ); 		
		
		foreach( $post_meta as $meta_key => $val )
		{
			if (strpos( $meta_key, 'brands_' . $count  ) !== false) 
			{
				$new_key = str_replace( 'brands_' . $count . '_' , '', $meta_key );
				add_post_meta( $pid, $new_key, $val[0] );
			}
		}

		global $wpdb;
		$wpdb->query("INSERT INTO  `wp_p2p` ( `p2p_id` , `p2p_from` , `p2p_to` , `p2p_type` ) VALUES ( NULL ,  '{$advertiser_id}',  '{$pid}',  'brands_to_advertisers' );");

		$count++;
 	}
 
 }