Everyone has assumed that they are one-and-the-same, because of this:

Then the woman struck back at her, and she suffered her second shock. She was stronger than Cyndane had been before the Aelfinn and the Eelfinn held her! That was impossible; no woman could be stronger. She must have an angreal, too.

Add in the fact that Cyndane apparently has all of the knowledge and feelings toward Rand/LTT that Lanfear would have, and it seems it's a cinch they are the same person.

Every glossary entry about the Forsaken varies, updating their current status. The last, most complete one, is from CoT. Here's an excerpt:

...Those thought to have survived are Demandred, Semirhage, Graendal, Mesaana, Moghedien, and two who were reincarnated in new bodies and given new names, Osan'gar and Aran'gar, although it seems possible that Osan'gar may also be dead. The life of a Forsaken is always uncertain. Recently, a man calling himself Moridin has appeared, and seems to be yet another of the dead Forsaken brought back from the grave by the Dark One. The same may be possible regarding the woman calling herself Cyndane, but since Aran'gar was a man brought back as a woman, speculation as to the original identities of Moridin and Cyndane may prove futile until more is learned.

We may be assuming too far about Cyndane, especially given that BS sidesteps the issue. Perhaps there is more to it than a simple transmigration and Healing. After all, we have seen the Finns transfer knowledge from others into Mat's head, so perhaps Cyndane is a similar instance, except all of Lanfear's memories have been transferred to another body. (And I'm not saying the Finns did it, either.)