User blog comment:Jiskran/Gideon and other trans-temporal anomalies/@comment-6331988-20150429203521

I'm guessing that since Barry created Gideon, Gideon knows about the Reverse-Flash and Eobard Thawne, so Eobard had to reprogram Gideon into thinking that he was actually Harrison. Since Gideon clearly respects Barry, I doubt she would be working with Eobard, if she knew his true identity.