Board Thread:The Flash discussions/@comment-11526603-20160401014522/@comment-11526603-20160401035334

Kaestal wrote: Umm.. those events hadn't yet occurred, and Eobard Thawne not returning to his time so as to eventually kill and replace Harrison Wells, create S.T.A.R labs, and become the mentor of Team Flash is what was killing Cisco as that timeline was being erased.

McGee wasn't really a factor in that. If we're going by the way you describe it then Barry, Caitlin and anyone else associated with Thawn would've also been affected. I think that Cisco was the only one affected because he was the primal cause of this effect.