Speaking to Den of Geek about the upcoming new season, Atwell said "there will be repetition of characters. So Jarvis and Howard will be there with us again. Yeah, we can't have a show without those guys."
James D'Arcy has already been confirmed to return as Edwin Jarvis, along with Enver Gjokaj as Agent Souza. It's also been explicitly stated that Peggy Carter and Jarvis will not be working of Howard Stark this time around.
It's possible that Atwell got this wrong, basing it on incomplete or out-of-date information, or it's possible that Cooper's return simply hasn't been officially announced yet. As Cooper would most likely be returning as a guest star, compared to D'Arcy and Gjokaj as series regulars, it makes sense that he wouldn't be included with the previous announcement.
Agent Carter will return to ABC during Agents of S.H.I.E.L.D.'s midseason break.