How to set value in Query Loop?

You can run multiple nested WP_Queries as long as you reset_postdata() to get the outer loop back on track.

$query_args = array (
    'posts_per_page' => '1',
    'meta_key'       => $count_today,
    'orderby'        => 'meta_value_num',
);

$outer_query = new WP_Query( $query_args );


while( $outer_query->have_posts() ) :

    // conditional if
    if( true ) {

        // change the query arg in the inner loop
        $query_args[ 'meta_key' ] = 'something_else';
    }

    // start an inner query with adjusted params
    $inner_query = new WP_Query( $query_args );

    // nested loop
    while( $inner_query->have_posts() ) :

        // ...

    endwhile;

    // After looping through a nested query, this function restores the $post global to the current post in this query.
    $outer_query->reset_postdata();

endwhile;