MySQL swap one table for another?

Create a php script ( fpw-swap-thumbnails.php ) with the code below and put it in root of your site:

<?php
// load WordPress environment
require( 'wp-load.php' );

$args = array(
    'posts_per_page' => -1,
    'post_type' => array( 'post', 'page' ),
    'post_status' => 'publish'
);

// get all published posts of type specified in $args
$posts = get_posts( $args );

foreach ( $posts as $post ) {
    // get thumbnails ids
    $thmbsArray = array(
        get_post_meta( $post->ID, '_thumbnail_id', true ),
        get_post_meta( $post->ID, 'post_secondary-image_thumbnail_id', true )
    ); 
    // if both thumbnails exist then swap their values
    if ( ( '' != $thmbsArray[ 0 ] ) && ( '' != $thmbsArray[ 1 ] ) ) {
        update_post_meta( $post->ID, '_thumbnail_id', $thmbsArray[ 1 ] );
        update_post_meta( $post->ID, 'post_secondary-image_thumbnail_id', $thmbsArray[ 0 ] );
    }
}
?>

NOTE: in post_secondary-image_thumbnail_id replace secondary-image with your registered secondary image id. In $args add any extra post types into post_type array.

Make a backup of your database ( just to be safe ). Execute the script. Check results. Remove the script.