I don't know if this will help you or not.I am descended from Annie Terry and Cornelius Estep (son of Shadrack Estep)I too have the family history of Native American heritage.I tested my MtDNA and was sure it would show Indian heritage, but it did not!
Still, I couldn't understand how so many Estep and Terry descendants who didn't know each other,could have the story of Native American ancestry and be wrong.
I think I have figured it out, though I have no absolute proof.This may seem a bit complicated, but it does work out.
MtDna is passed from mother to daughter to daughter.Y DNA is passed from father to son to son, etc. So, here is my speculation....
Cheapoke Harris (native american) married Trapper Terry and they had Miles Terry...Miles' sisters (1/2 Indian) would have Native American DNA from their mother, but Miles(also 1/2 indain) would have his father's non-indian Y DNA and would pass this on to his sons.Mile's daughters would have Hanna Horton's non-Indian MtDNA even though their grandmother on their father's side was a full blooded Cheraw or Cherokee.
So, even though we have Native American ancestry, It won't show up in the Y DNA or the MtDNA of certain descendants.It will show up in direct descendants of Chepoake's daughters.