⚡ Quick Fix (TL;DR)

The Culprit: Sorting a WP_Query by meta_key plus orderby: meta_value (or meta_value_num) uses an inner join on the postmeta table. Any post that doesn't have that meta key at all gets silently excluded from the result set – not sorted to one end, removed entirely. This happened twice independently on the same site: once for an existing Stage column, once for a brand-new column, both with the identical structural flaw.

The Fix: Add an explicit meta_query with an OR relation combining an EXISTS clause and a NOT EXISTS clause for the same key. This is WordPress's own documented pattern for keeping every post in the result set regardless of whether it has a value to sort by yet.

$query->set( 'meta_key', 'your_meta_key' );
$query->set( 'orderby', 'meta_value' ); // or meta_value_num

$query->set( 'meta_query', array(
  'relation' => 'OR',
  array( 'key' => 'your_meta_key', 'compare' => 'EXISTS' ),
  array( 'key' => 'your_meta_key', 'compare' => 'NOT EXISTS' ),
) );