Melora = Ehlonna.
You're not wrong, which is why I wondered if Eilistraee may have "absorbed" Melora upon her return.
It's all DM specific, really, which I get. I have plans of playing a Half-Drow follower of Melora, and Eilistraee is an excellent fit for the vision I had for her. In our campaign, the Drow aren't all Evil, just tribal and misplaced and the DM has established that all the elves used to be of one creed.
Also, as an afterthought - maybe the 4e's Wellblade (Hexblade with the Well pact) imprisoned Goddess could be this Eilistraee? That would be amazing, as this character's father is a Wellblade (and also my current PC)!
Ehlonna is a Greyhawk deity though, not a Realmsian one. And she's really not that great of a fit for Melora - there's some overlap, yes, but if I was converting an adventure featuring Melora stuff to Greyhawk I would probably use Obad-Hai (for land-based things) or Procan (if it's sea-related).
Ehlonna'a portfolio is considerably narrower than Melora's - Ehlonna's about the woodlands and its inhabitants, whereas Melora is about all sorts of nature. Ehlonna also has a more "positive" outlook on nature (from a human perspective) than Melora - she is Neutral Good whereas Melora is Unaligned (OK, different alignment systems, but I'm pretty sure Ehlonna would be Good in 4e). Ehlonna wants a romantic ideal of nature where humans and animals frolic together in the forest, whereas Melora also represents nature's more destructive aspects.
In 4e's White Well story, Lolth (then Araushnee) tricks Sehanine into 'cheating' on Corellon by disguising herself as Corellon; the White Well lady is the result of this union. Corellon is ticked at Sehanine's infidelity and locks the daughter in the Well.
In FR Canon, Eilistraee is also the daughter of Corellon and Araushnee.
Admittedly we're not going to follow FR canon, but my DM seems to like the idea and that's how we're playing it at our table.
Eilistraee is thus going to be a demigod tied to Melora's "camp" via their common hunting/wilderness angle and will also resume her mantle as one of the Seldarine.
It's a homebrew setting. The only connection Melora is going to have to Eilistraee is that, previous to becoming a Dark Maiden, my character was formerly an Acolyte (but not priestess) of a Meloran temple. The attachment between the two is tenuous at best, as you said, but in our game Melora is the only "verified" and True Deity while the rest of the world's faiths remain mostly agnostic.
In other words, some Melorans (specifically the ones who favor her Wilderness aspect) may branch off and become Eilistraee cultists; this will likely be one of my character's goals. The Seldarine are established as the centre of Elven lore/belief and while they are not Deities themselves, they are Immortal Elves Of Great Power and Wisdom as one might expect.
How this affects the world at large (or at all) is entirely in the hands of the DM.