The Yabunouchi family was also affected by the upheaval of the end of the Edo period, and the residence was completely burnt down during fighting in 1864; however, it was soon rebuilt thanks to the support of Nishi Hongan-ji Temple, which had been its benefactor since the Shino's time.
幕末の動乱は藪内家にもおよび、元治元年（1864年）の兵火で家屋は全て焼失しているが、真翁以来の庇護者であった西本願寺の援助によって速やかに復旧を遂げている。