Having same problem. Ended up with the following codes
global $woocommerce_loop;
$woocommerce_loop['paged'] = (isset($woocommerce_loop['paged'])) ? $woocommerce_loop['paged'] : 1;
$woocommerce_loop['total'] = $custom_query->found_posts;
$woocommerce_loop['post_count'] = $custom_query->post_count;
$woocommerce_loop['per_page'] = $per_page;
$woocommerce_loop['total_pages'] = ceil($custom_query->found_posts/$per_page);
$woocommerce_loop['current_page'] = $args['paged'];
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