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I don't think we need to address the Eobard Thawne RF erasure from time. The RF in season 2 is Dr. Stein from Earth 2. At 2 different points (when 1st arriving at/in Earth Prime and after watching Flash disable the rigged 18 wheeler) Gideon refers to this RF as "Dr. Stein." Therefore, this RF is from a different dimension and the erasure of Eobard Thawne from Earth Prime timeline does not affect him.
Can anyone else confirm that bit about Gideon saying Dr. Stein is Earth-2's Reverse Flash? Because I don't remember hearing it or seeing anyone else mention it anywhere.