Barry’s disappearance been known since the first future paper, as The Flash disappears following a big battle with Reverse-Flash.
In the hypothetical scenario where he vanished as well, Reverse-Flash has time remnants of himself placed across different periods.
It’s completely possible a time remnant of Thawne could be around to influence Nora, and this could be the beginning of a sequence of events that lead to Barry’s disappearance.
While Barry never returns, the fate of Reverse-Flash is unknown.