I agree with Mira. Also, looking at the way Ebenezer freaked out and attacked Lara in Turn Coat, when Lara said she was going to travel with Harry, I'm pretty sure Harry made the right decision not telling Eb about Thomas earlier. It just wasn't going to go well.
Even if in a later book Thomas should show up in front of Ebenezer as a KotC, I feel fairly certain that Eb wouldn't believe what he was seeing. Not right away.