Add custom ID to CPT posts only create not update

Yes, it’s simple – check for existence of id_valoraciones meta value when saving post. If post does not have id_valoraciones set, do your job with getting last value and incerementing it. If the post has id_valoraciones meta, then – do nothing. Like this:

<?php
function auto_assign_ids( $post_id, $post, $update ) {

    // Only assign ID to new approved "valoraciones" posts
    if ( $post->post_status == 'publish' && $post->post_type == 'valoraciones' ) {
                
        $id_valoraciones = get_post_meta( $post_id, 'id_valoraciones', true );
        
        if( ! $id_valoraciones ) {
            
            // get the most recent "valoraciones" posts
            $valoracion_args = array(
            'numberposts'       =>   2,
            'post_type'         =>   'valoraciones',
            'orderby'           =>   'post_date',
            'order'             =>   'DESC'
            );
            $valoraciones = get_posts( $valoracion_args );

            // get the id_valoraciones of the prior post
            $last_id = get_post_meta( $valoraciones[1]->ID, 'id_valoraciones', true );

            // increment
            if ( !$last_id ) {
                $last_id = 0;
            }       
            
            $last_id++;
            
            update_post_meta( $post_id, 'id_valoraciones', $last_id );
            
        } else {
            
            // id_valoraciones was set before
            
        }
        
    }
}
add_action( 'save_post', 'auto_assign_ids', 100, 3 );

By the way, remove_action part of your code is useless, update_post_meta does not trigger save_post hook, it’s used when wp_insert_post()ing inside save_post hook.