This plugin makes All Access passes ignore repeat file downloads so that the download limit controls the total unique downloads.
<?php
/*
 * Plugin Name: EDD All Access - Do Not Count Re-Downloads
 * Description: This plugin makes All Access passes ignore repeat file downloads so that the download limit controls the total unique downloads.
 * Author: Pippin Williamson
 * Version: 1.0
 */

function pw_edd_aa_do_not_count_repeat_file_downloads( $do_count, $all_access_pass, $download, $requested_file, $email, $log_id ) {

	global $edd_logs;

	$logs = $edd_logs->get_connected_logs( array(
		'post_parent'            => $download,
		'log_type'               => 'file_download',
		'posts_per_page'         => 2,
		'update_post_meta_cache' => false,
		'update_post_term_cache' => false,
		'meta_query'             => array(
			array(
				'key'   => '_edd_log_payment_id',
				'value' => $all_access_pass->payment->ID,
			),
			array(
				'key'   => '_edd_log_file_id',
				'value' => absint( $_GET['edd-all-access-file-id'] ),
			)
		)
	) );

	if( $logs && count( $logs ) >= 2 ) {
		// This file has already been downloaded, do not count it again
		$do_count = false;
	}

	return $do_count;

}
add_filter( 'edd_all_access_download_should_be_counted', 'pw_edd_aa_do_not_count_repeat_file_downloads', 10, 6 );
To implement this snippet on your site, create a brand new, empty WordPress plugin and paste the above code inside.