Update taxonomy value of post type in query

There are quite a few steps involved here and also, with that 5000 posts figure you are mentioning, this will be an expensive task to do it through WordPress itself. However, here is what I came up with (I haven’t tested this so you may wish to use it on a backup first and see if it works):

global $wpdb;

/* The ( 'from_term_id', 'to_term_id' ) map. */
$terms_map = array(
    '3845' => '1248',
    /* ... The rest of your mapping */
);

$taxonomy = 'country';
$obj_terms = wp_get_object_terms( $post->ID, $taxonomy );

/* Loop through each object term */
foreach ( $obj_terms as $term ) {
    /* See if the obj term_id is a key in $terms_map */
    if ( isset( $terms_map[$term->term_id] ) ) {
        /* We have a valid key. We now need the term_taxonomy_ids */
        /* for both 'from_term_id' and 'to_term_id' */
        $to_term = get_term( $terms_map[$term->term_id], $taxonomy );

        $from_term_tax_id = $term->term_taxonomy_id;
        $to_term_tax_id = $to_term->term_taxonomy_id;

        /* Update the '{prefix}_term_relationships' table */
        $update_res = $wpdb->update( 
            $wpdb->term_relationships, /* The table to update */
            array( 'term_taxonomy_id' => $to_term_tax_id ), /* Data to be updated */
            array( 'object_id' => $post->ID, 'term_taxonomy_id' => $from_term_tax_id ), /* Where clause */
            array( '%d' ), /* Format of the data is int */
            array( '%d', '%d' ) /* Format of the where clause is int */
        );

        /* Finally, you may wish to update the term count for each term */
        wp_update_term_count( array( $from_term_tax_id, $to_term_tax_id ), $taxonomy );
    }
}

Like I’ve mentioned though this may prove to be too expensive in which case you will have to write a separate PHP script and work directly on the database.

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