In an interview with Den of Geek, Smith revealed he will be back at the directorial helm around mid-season.
"I know I'm going back to The Flash, first week of September, to direct episode 7 of season 3. Still haven't heard anything back from Arrow. You know, I wish, it would be amazing because I would love to write and direct Onomatopoeia in the show. Um, but I know they're doing – what is it? – Wild Dog this year, as well as Vigilante, so maybe they're just like 'we don't need you', or whatever. But, at the moment, anyone over there raises a flag; I'm like 'please, let me in!' That'd be fun as f***."
While we don't know what that episode will deal with, it is seems likely that issues pertaining to Flashpoint will factor into Smith's episode. He has also discussed previously how he would rather direct someone else's episode as opposed to writing and directing at the same time. Zack Stentz wrote the previous Smith episode, and there is talk of him possibly working on this one as well.
As for Arrow, depending on how things go with Onomatopoeia, the villain could always surface on The Flash later down the line.
"Even if they don't, maybe I could do it on Flash, or Legends Of Tomorrow, or now Supergirl as well. There's a couple of shows there."
He certainly does have several options at hand.