It can be done automatically if the format of your download link is always the same.

1. Backup your database

2. Create a php file named my-cleanup.php.

   Loop over all products, grab the link from the description and move it to a post_meta.

3. Launch the file with WP-CLI:

   wp eval-file my-cleanup.php

Sample code

// Select the posts you want
$args = array(
\'post_type\'      => \'post\',
\'post_status\'    => \'any\',
// -1 means all posts
// For debug, set this to a small number
\'posts_per_page\' => 3,
);
// Retrieve posts
$query = new WP_Query( $args );
$posts = $query->posts;
// Pattern to match
// [wpdm_package id=\'90228\']
$pattern = \\\"/(\\[wpdm_package id=\'\\d+\'\\])/\\\";
// Process posts one by one
foreach ( $posts as $post ) {
echo \\\"Processing \\\" . $post->post_title . \\\"
\\\";
$post_args[\'ID\'] = $post->ID;
// Get the shortcode from the post content
preg_match( $pattern, $post->post_content, $matches );
// Do we have a match?
if ( count( $matches) > 0 ) {
// Retrieve shortcode
$shortcode = $matches[0];
// Convert shortcode, maybe add some HTML
$link = do_shortcode( $shortcode );
// remove shortcode from description
$post_args[\'post_content\'] = preg_replace( $pattern, \'\', $post->post_content );
// Update post
wp_update_post( $post_args );
// Create the post_metas
add_post_meta( $post->ID, \'_download_link\', \'field_5cffd35335ce3\', true );
add_post_meta( $post->ID, \'download_link\',  $link, true );
}
}

Notes

1. Backup your database

2. Test on a few posts to get confidence in your code. You can restore the previous revision in the editor.

3. Then try on 100, then 1000. You will often find small differences in the way posts are entered.

4. This might take hours to run on 10.000 posts, which is why you need a WP-CLI command.