Wells has had cameras in every location of note. He was monitoring what the scoobies were planning. And Cisco ' sCisco's very vivid lucid dreaming included all the details he needed to know in order to have Everyman recreate the scene close enough to scare Cisco who only half remembered it.
Additionally, in both comics and the show, Eobard, like most speed force speedster are somewhat immune to time changes, similar to how Cisco was portrayed. Flashpoint Paradox is a prime example. Zoom who was not involved in Barry's saving his mom, had no memory loss from the alternative time line.
finally, Gideon, the advanced A.I. is able to track changes in the timeline. This can help Wells fill in any holes from what he learned from Cisco's recorded dream.