Board Thread:General Discussion/@comment-29082320-20160731164526/@comment-27701762-20160731165254

It's not quite clear that Chara's soul is with Frisk. There is a weird connection between Chara and Frisk, and a lot of people posit that Chara exists as a sort of spirit that is awakened and lingers around Frisk once they fall into the Underground. Instead of Frisk having Chara's soul, Frisk is simply using their own soul, which just happens to be red, just as Chara's was. Chara's soul itself was, presumably, lost when Asriel died, and it was not captured, since it is not among the captured souls that Asgore has (otherwise he wouldn't need to kill Frisk for the seventh soul).