Thats a tough one, but I wouldn't doubt that the Uchiha Clan, area in the Hidden Leaf would be raided and then completely wiped out, and that SOMEONE would discover the secrets in the area, and may have brought them to either the Hyuuga Family, or Hokage at the time... Either one could study said secrets, (Documents, as far as I remember the Bloodline had a Chart for what Tomes meant what stages the Sharingan was at.)
One the documents would have been reviewed, the Hyuuga (I don't care if it's spelt wrong!) would realize the importance of having the Sharingan users... And attempt to recreate the Sub-Branch again... As with the Rinnengan, the bloodline would Surface someone far down the line, possibly not related or even forgotten, into the Uchiha clan. Example, the Uchiha could be a kiddnapped, or held hostage member who was freed long ago and began to recreate the Uchiha clan.
Question: What would happen if you crossed the Sharingan with the Byakugan? Would the Eye become completely insane?