Thawne himself in this story said that he had been dead and would remain dead for awhile. Clearly, there is convoluted time going on, and he is partly aware of it. Of course, in most if not all of those scenarios, he ends up dying centuries before he is born.
As I noted, the bloodstains on his uniform are absent when he reappears, dying. I suspect that we'll find out that the dying Thawne came from before or way after or another timeline than the one who fought Batman. FYI, there are several unchanging panels during his absence to indicate that time is passing, but it must not be very much time because it's only the amount that Barry Allen is later than he planned.