Board Thread:Theories and Speculation/@comment-30168130-20170115054258/@comment-30426414-20170120020657

Naruto didn't lose his last 3 TSB's, he still had them during the indra's arrow vs rasenshuriken clash. After the clash, the explosion caused him to deactivate his six paths sage mode thus deactivating the TSB's in turn. So he never really lost the last 3.