I went back and looked over the history of Felicity and Ray's relationship, and I think there's only one place where this makes any sense at all - This happens sometime the time between S03E15 "Nanda Parbat" and S03E16 "The Offer".
There's a couple of things that I think make things fit here:
- During the course of "Nanda Parbat", Ray and Felicity really solidify their relationship, showing a lot of mutual trust and caring between them, not to mention sleeping together for, I believe, the first time. In STAR Labs, Felicity is quick to point out that there is "nothing wrong in the sex department" between her and Ray.
- At the end of "Nanda Parbat", Ray finishes the suit and goes flying around in it. By the next time we see him using the suit on Arrow, he seems to have pretty good control over it. Certainly, he doesn't show the erratic flying behavior he does in "All-Star Team-Up".
- During Nanda Parbat, Oliver once against leaves to confront Ra's Al Ghul; this causes a lot of tension and drama amongst Team Arrow. In Central City, Felicity says she left Starling City to "get away from the drama".
- At the end of "The Offer", Ra's shows up in Starling City and starts killing people, posing as The Arrow. After that, it's unlikely that Felicity would feel comfortable leaving Oliver in Starling City without her.
- By the end of the next episode, "Suicidal Tendancies", we start to see the beginnings of a "rough patch" in the relationship, which doesn't match up with their relationship in the Flash episode.
So, my best guess is, when Oliver ran off to Nanda Parbat, Felicity took the time to visit Central City and focus on helping her new boyfriend with his per project, leaving Team Arrow to deal with their Ra's/Malcom/Oliver mess on their own.