Here you'll find all that you need: http://forgottenrealms.wikia.com/wiki/Eilistraee#Rebirth
Eilistraee managed to return to life during the event known as the Sundering, in Flamerule, 1489 DR. She and her brother were separate entities again, but after the time spent as the Masked Lady, they reached a reciprocal understanding, and the enmity between them was no more. Both deities personally let their return be known, manifesting through their avatars to their followers, who enthusiastically spread the word. Eilistraee was seen dancing and speaking to mortals in many places, especially along the Sword Coast. For example, the citizens of Waterdeep witnessed the Dark Dancer, as she danced in the moonlight, near the walls of the city, up the road to Amphail. This led many moondancers to the City of Splendors, with the goal of creating a shrine to their goddess within its walls.
Eilistraee was also one of the deities with whom the returned Mystra was sharing the Weave after the Sundering.
Eilistraee accepts male clerics after the Sundering. Vhaeraun is also back (as said above).
In one of his answers, Ed Greenwood suggests that Eilistraee actually spared her brother's life. The Dark Maiden defeated Vhaeraun with the indirect help of her ally Mystra, as the Weave frustrated the Masked Lord's magic while enhancing Eilistraee's. The goddess temporarily took her brother's portfolio, and trapped his sentience in the Weave, where it was enfolded in a dream by Mystra. The Lady of Mysteries did that to ensure that the two drow siblings would survive the cataclysm that she knew was coming—the Spellplague—in which she would be "killed" to renew the Weave, and magic would go wild.
In the same answer, Ed Greenwood hints that Eilistraee actually managed to survive Halisstra's attempt to kill her, albeit much weakened. When Qilué Veladorn was killed, since the Masked Lady was inhabiting her body, a great part of her power was dragged into the Weave with the Chosen's soul (the souls of Mystra's chosen often become "Voices in the Weave" after their death, as explained in the novel Spellstorm, and their memories and experiences are shared by Mystra). After that, for about a century, Eilistraee could only manfest herself only as a floating black mask surrounded by moonlight, capable of silently communicating with mortals, but not of answering prayers or granting spells (except by direct touch). After Mystra and the Weave were completely restored in 1487 DR, the goddess of magic could finally give Eilistraee her own lost power, and do the same with Vhaeraun, after having awakened him from his dream.
As for the dark elves, they were very few, so it's natural that they kinda dropped off the map (consider that WotC created them only because they wanted any non-Lolthite drow to be gone back then, and then they said absolutely nothing about them. Add to that the fact that the transformation has nothing to do with Eilistraee and her goal, it even diminishes it, and you get the pircture. http://forum.candlekeep.com/topic.asp?TOPIC_ID=19597.
As of the 1490s DR, post Second Sundering, the returned goddess Eilistraee still had many drow followers despite a century of absence. Considering that the transformed drow were less than one thousand, and that the Dark Maiden, as a lesser power, had at least a few thousands of followers, this could lead to think that there is a possibility that Q'arlynd's spell didn't in fact affect all the followers of the goddess, or that they were given the choice to embrace the transformation or not.[speculation]
Eilistraeeans have also established a presence in the reclaimed ruins of Maerimydra.
During the event known as the Rage of Demons, a group of Sword Dancer of Eilistraee, led by the charismatic and kind-hearted high priestess Saradreza Oussmtor, decided to help an unlikely coalition (composed by agents of the Harpers, Zhentarim, Emerald Enclave, Lords' Alliance and Order of the Gauntlet; by the drow of Szith Morcane, led by archmage Solom Ned'razak, the warriors followers Elanil Elassidil of the Hillsfar rebellion, the Red Plumes guided by First Lord Vuhm Yestral, the myconids of Sporedome, and the illithids of Ryxyg) to oppose Graz'zt's growing influence in Maerimydra. The demon lord had in fact rallied the fire giants led by his daughter Hledh Hellspawn, and turned Maerimydra into a base from where he would work to spread his demonic influence and gain control over the Material Plane (through a restored Undying Temple, which he planned to use to gain free access to the whole prime--surface included). His threat had already taken a heavy toll on the drow of Szith Morcane and in the area of Elventree and Hillsfar, leading unlikely allies to band together to face demons and giants.
The followers of the Dark Dancer saw this as a good opportunity to lend their help, and spread the message of Eilistraee among other drow who were tired of Lolth's tyranny. The alliance would eventually succeed, and Saradreza and the other Sword Dancers would have the opportunity to gain a place in Maerimydra alongside the drow of Szith Morcane, from where they hoped to establish good relationships between the drow and the other inhabitants of the Moonsea area.
Sources: Sword Coast Adventurer's Guide (essentially every god ever has been resurrected); Ed Greenwood's Death Masks and Spellstorm; Ed Greenwood's answers over Candlekeep; Assault on Maerimydra (adventure).