how to skip a CPT element from the pager by custom field

It looks to me like you’ve gone too deep with your meta_query argument. The meta query should be an array of arrays; you’ve got an array of arrays of arrays.

Try:

$args['meta_query'] = array(       
    array(
        'key'   => 'status',
        'value' => 'Retained',
        'compare'   => '='
    )
);

References

• WP_Meta_Query class (which is used to parse the meta_query argument for WP_Query)