When "The Flash" returns for Season 3 this fall, so will Tom Cavanagh. According to Entertainment Weekly, Cavanagh will be back as a season regular, though it's unclear at this time just who he'll be playing.
Over the past two seasons of the show, Cavanagh has played two separate characters: in the first season, he was Eobard Thawne, aka Reverse Flash, masquerading in the form of Earth-1's Harrison Wells; and in Season 2, he played Earth-2's version of Harrison "Harry" Wells. However, in the Season 2 finale, he and his daughter Jesse returned home to Earth-2 with the help of Earth-3's Jay Garrick.
However, as the report points out, Cavanagh could be playing an entirely different character thanks to the events of the Season 2 finale: the original Earth-1 Harrison Wells. In the finale, Barry went back in time and stopped Reverse Flash from murdering his mother, meaning he has upset time as he knew it. As such, it's entirely possible that Reverse Flash never went on to murder Wells and his wife.