Usually when an in-game thing like a feat, magic item, spell, or, like in this case, a cleric domain gets reprinted in a later text, that later text’s version of the thing takes precedence over all previously published versions of the thing.
Then there’s the Darkness domain. It was introduced, reintroduced with commentary, renamed, then, finally, without commentary, reintroduced again.
Here’s how it went: The Book of Vile Darkness (Oct. 2002) introduces the domain Darkness (80). Then Player’s Guide to Faerûn (Mar. 2004) presents a Darkness domain (85) that has different spells from the Book of Vile Darkness domain of the same name, but the Guide says, “A cleric who has access to the Darkness domain [from any of the deities Graz’zt, Lolth, Mask, Set, Shar, and Shargaas] can use either the Darkness domain presented in… this book or the one in Book of Vile Darkness” (189).
But then Lords of Madness (Apr. 2005) presents the domain Vile Darkness which is like the domain from the Book of Vile Darkness, and it says, “This domain description is a revision of the Darkness domain presented in Book of Vile Darkness” (208). Finally, without commentary, the Spell Compendium (Dec. 2005) presents again the domain Darkness (272), like the one from the Player’s Guide to Faerûn, but the Compendium doesn’t mention the Book of Vile Darkness at all.
Now,—and I apologize for this hinging on technicalities and minutiae like primary sources and publication dates—, here’s the question: Does the Spell Compendium‘s Darkness domain replace all previous iterations of the Darkness domain, including, possibly, the original Darkness domain from the Book of Vile Darkness (which received neither errata nor a 3.5 revision), therefore rendering obsolete the Lords of Madness domain Vile Darkness?
Specifically, Lost Empires of Faerûn (Feb. 2005) says that clerics of Ibrandul—the dead god of caverns, dungeons, and (I guess because somebody had to be) skulks—are granted access to the domain Darkness (41), and I don’t know if such clerics should have access to the Lords of Madness domain Vile Darkness, the Spell Compendium domain Darkness, or both.
Note: While this question may sound trivial, and although they offer the same granted power (the feat Blind-fight as a bonus feat), the Lords of Madness domain Vile Darkness offers a much different selection of spells from the Spell Compendium domain Darkness. Also, while a dnd-3e source, the Book of Vile Darkness never received an official 3.5e revision, hence the inclusion of both tags below; note, however, that I am concerned only with this question’s impact on 3.5e campaigns. As for why this question even arose, see this question.