GW have a habit of rewriting history. Just because there is detailed background out there, the fact that it hasn't been touched (and barely referenced) for fifteen or twenty years leaves it ripe for GW to redesign. See the latest Tyranid codex as an example of this retrofitting.

Well the history and reason for existing is pretty stable. I cannot see the 'Cult' changing in any way as the example you have given. They will either never come back and be written out of history, or they will be back as before.

Either way, it is not a concern for the development of the GS Cult list. Procrastination is far worse than a GW rewrite.

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I'm not suggesting it as a reason for concern, just noting that it's possible that it could happen, much as it seems possible that Xenos' Demiurg fluff could be contradicted by the new tau codex.