I had a similar problem where the checkbox had been checked, creating the key, and then being unchecked at a later time. I seemed to have fixed it with this (‘rented’ is the checkbox field):
'meta_query' => array( 'relation' => 'AND', array( 'key' => 'status', 'value' => 'active', ), array( 'relation' => 'OR', array( 'key' => 'rented', 'value' => '1', 'compare' => '!=' ), array( 'key' => 'rented', 'value' => '1', 'compare' => 'NOT EXISTS' ) ) )
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