Rewrite the WP-Shopify (https://wpshop.io/) post types to retain their permalink structure if a custom post type structure is set.

wps_rewrite_post_type_args.php

<?php
/**
 * wps_rewrite_post_type_args
 *
 * Retains the permalink structure if a custom permalink structure is
 * set within Wordpress.
 * 
 * @param  array  $args      Wordpress post type arguments.
 * @param  string $post_type The post type's slug.
 * @param  array  $settings  The plugin settings data pulled in from the DB.
 * @return array  $args      Modified wordpress arguments.
 */
function wps_rewrite_post_type_args( $args, $post_type ) {

	global $wpdb;

	$slug = false;

	// retrieve the plugin URL settings
	$settings = $wpdb->get_results( "SELECT `url_products`, `url_collections` FROM wp_wps_settings_general" );

	if ($post_type == 'wps_products') {
		$slug = $settings[0]->url_products;
	} else if ($post_type == 'wps_collections') {
		$slug = $settings[0]->url_collections;
	} else if ($post_type == 'wps_orders') {
		$slug = 'orders';
	}
	if ($slug) {
		$args['rewrite'] = array(
			'slug' => $slug,
			'with_front' => false
		);
	}

	return $args;

}
add_filter( 'register_post_type_args', 'wps_rewrite_post_type_args', 20, 2 );