Those conquered Emishi people weren't completely wiped out or disappeared during Yamato's " eastward expansion ",I believe they blended in or assimiliated into the general population except for the ones
they were not living in only tohoku area
they were living in whole japan.

for example, saeki clan
http://ja.wikipedia.org/wiki/%E4%BD%...BC%AF%E6%B0%8F

I think that in process of　their moving to the warm place, hokkaido ainu was isolated