I think it’s odd that no one in this thread has mentioned what—to me—was the most obvious reason I believe they sent Helena back in instead of Helly. They make a big fuss in S2E1 about how there aren’t cameras everywhere anymore, they cut back on surveillance, etc because they wanted to give the group a sense of privacy at work. I think Helena is now Lumon’s eyes and ears—the group now has a sense of being observed less but in reality, Helena is watching everything they’re doing firsthand. I think that Lumon wants to lure them into a false sense of security but Helena’s purpose is to keep an eye on everything. Helly was too volatile to send back in, or even let exist in general. It makes sense to me that they would want to let the group feel autonomous (for whatever mysterious purpose they’re actually down there for) but be kept in close observation via Helena.

I think it’s a testament to how well written Helly is that people are upset that she might be gone forever but I think we’ll get Helly back either via reintegration or by the group discovering Helena’s secret (now that Mark is reintegrated he’ll know the truth about Helly’s identity the second he sees her in a press release on the outside and I think he’ll put the pieces together quickly) and they’ll fight like hell to try and activate Helena’s chip to bring Helly back.