Board Thread:The Flash discussions/@comment-9346948-20161130010008/@comment-3221148-20161130093927

Before, Cisco did not know if Dante died in the previous version of the timeline, since Barry allowed to give everybody a choice if they wanted to hear whether there were changes or not. All he knew is that Barry had no recollection of his "refusals to change the timeline for Dante".

Now, Cisco just recently learned that Barry's (or, rather, Eobard's) time travel is directly responsible for this change happening, and for no reason. Understandingly, he's upset and, at his own admission, not sure if he can ever be friends with Barry after that.

It doesn't make logical sense if you know all the facts, but on an emotional level, to Cisco, it's as if Barry just confessed to murdering his brother.