Instead of trying to help defeat The Flash, Barry’s greatest enemy returned to provide assistance with Godspeed and August, and while Nora and Bart didn’t understand why their father asked for Reverse-Flash’s help rather than theirs, Barry was more than understanding.
Since Thawne’s ideal future is such where HE’S the one who gets to defeat Barry, it was only normal for him to help with the Godspeed sitch so that he can go back to scheming and trying to eliminate The Flash once and for all on his own terms.
Plus, this way, Nora and Bart were out of harm’s immediate path.