Actually, because Kyoto Shoshidai, whose job was to monitor and negotiate with the Imperial Court, was governing from a mansion to the north of Nijo-jo Castle, in the Shogun's absence the castle was not used at all as an office of the Shogunate government.
なお、朝廷の監視および折衝を担当する京都所司代は二条城の北に邸を構えそこで政務を執っていたため、将軍不在の二条城は幕府の政庁としては全く使用されなかった。