With Barry in the past, I have a feeling that they will have him prevent Joe being kidnapped, meaning that Iris' confession and him revealing himself as the Flash to her do not happen, so those two things get reset to the previous status quo of this season.
Now the question is if this changes Cisco's path at all. Perhaps Eobard handles it differently if he knows Barry now can travel through time, which the previews look like Barry talks to him about that. Or Barry having them help prevent Joe's kidnapping delays/distracts Cisco's research, so that scene does not happen.
Wells/Thawne did indeed seem pleased when Barry mentioned that he saw a mirror image of himself as he was running, so he likely knows Barry has now started to hit the time warp speeds.
Also this story looks to be the one where Barry first time travels and then experiments to see if he can change things. Of course given that we are only looking at 24-48 hours of time change the overall effect on history would be minimal.
His goal is to go back 15 years and make a rather significant change.