This method only works if the WPSP list is displayed on the page. It’s not on the paginated page, so the code doesn’t know to exclude it from the archives.
If you know the IDs of the posts you want to exclude, you might be able to get away with just this:
add_filter( 'generate_do_template_part', function( $do ) {
$excluded_post_ids = array( 1, 2, 3 );
if ( in_array( get_the_ID(), (array) $excluded_post_ids )) {
$do = false;
}
return $do;
} );
Just replace the 1, 2 and 3 with the IDs you’ve manually set in your WPSP list.