Well, TVTropes itself says she was
Put On A Bus, which is the main category that the Chuck Cunningham Syndrome is under, so yeah, she's gone, but someone could bring her back. Honestly, seeing as how he saw her more as a tool to get what he wanted, even going as far as giving her up to Brainiac 13 in exchange for the B13 technology, which he used, in part to get elected president, it's not too much of a stretch to assume he gave her away when she became more trouble than she's worth.
If she were to show up again, I would assume Cornell would work her into his
Action Comics arc with Luthor, though seeing as how that's only got a few months left, I wouldn't hold my breath.
While the potential for stories exist, I think Lena, like PeeGee's son, is too much trouble to bring back and explain where they went to do so without a really good story backing it up. Cornell, in my opinion, is a good enough writer to do it, though.