Board Thread:Theories and Speculation/@comment-27260817-20160203170532/@comment-734582-20160204200008

Ravenlot 27 wrote: There's no evidence Naruto lost either the TB chakra, or Hagoromo's chakra at all. All chakra gifts are temporary. Every single gift of chakra has always expired upon use.

That's not to say their powers receded, since Hagoromo was also the guy that turned a bunch of chakra into nine individuals with unique powers and appearances. It's safe to say that abilities he gives are permanent.

But there's also this: Hagoromo clearly has his Sage Markings, Madara had it and recreated his chakra, Naruto had it after Hagoromo gave his chakra. So it stands to reason that if he used up the -again finite- chakra gifts, Hagoromo's markings also disappear.