Eu diria que não. Um combatente não pode fazer ataques de oportunidades e não ameaça nenhum quadrado.
Total Defense You can defend yourself as a standard action. You get a +4 dodge bonus to your AC for 1 round. Your AC improves at the start of this action, so it helps you against any attacks of opportunity you incur during the round. You can’t combine total defense with fighting defensively or with the benefit of the Combat Expertise feat (since both of those require you to declare an attack or full attack). You can’t make attacks of opportunity while using total defense.
Flanqueando, declara especificamente:
When making a melee attack, you get a +2 flanking bonus if your opponent is threatened by a character or creature friendly to you on the opponent’s opposite border or opposite corner.
O combatente precisa estar ameaçando o oponente, e enquanto estiver usando defesa total, o combatente não está ameaçando.