Wasn't the leg trap thing supposed to stop his speed entirely or was it just his legs? Either way, it didn't work, but on E-2 wasn't Jay being the Flash and saving people for like a year? Maybe a good Jay Flash somehow breached E-2 and couldn't figure out how to get back (Similar to Thawne) so he stayed and Zoom figured out how to steal speed at that point and that's who he has in the iron mask?
Thawne knew who Jay was so he was probably from his timeline, but then again maybe not cuz he was there to kill Barry's Flash....
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