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It seems like all of the Fallen are pretty much Dark Angels models painted black, but fluff-wise, would it make more sense for them to use the CSM codex or the DA codex?

CSM or SM would make the most sense, since the DA codex DA have regressed / evolved separately from their "fallen" brothers . So why not use the actual rules for them and just ally in the rest of the "army" using battle brothers rules.

Could you elaborate a bit? I'm not quite sure what you mean by using their actual rules.

There are rules for them in the latest gathering of the storm book. But its just one unit, faction rules and cypher you will probably want more than just dudes so allying the big machines in makes sense.

Fallen Dark Angels are fairly rare, having been scattered through space and time I imagine it is unusual for large groups of them to be gathered in one place.

Furthermore, such a gathering of Fallen would be rather inconspicuous and likely to draw attention quickly.

For these reasons, you will need to put a lot of thought in to how your group of Fallen came together, and for what reason they operate together. An army of Fallen is unlikely to 'just happen'.

This opportunity for creativity means you get to decide how your Fallen army will be structured and function, and as such which rules best represent them

If you are planning on painting some Fallen, what is your story behind them? How many of them are there? Have they been together since the destruction of Caliban, have they come together over the years?

Is the army a HH era sergeant and his squad (now lord and chosen) leading his entourage of human followers (the survivors of the world his squad landed on and subjugated)?

What he meant is that they have their own faction and rules. The newest being in the latest gathering storm book. But like he said, it's not exactly an army. I'm not sure of the data slate is still technically valid, but if it is, that's another (older) source.

The old cypher could not be taken in the any army that has dark angel models in it. I can't remember if that was changed to detachments now, but yea. Either way they don't play well with dark angels so you'll want to avoid that. They can be used in any army of the imperium or chaos space marines, but the dataslate and the gathering stom book have their own profiles listed for the fallen as well as cypher, so you need neither codex for those particular units.
You ARE going to want to use them in a different army though because you're not going to have a good army with JUST fallen, least not unless it's a small points game.

Alternatively, if you want an army of fallen then I suggest you use the Horus heresy list instead. Nobody is going to give you trouble for using the gathering storm/dataslate fallen along side a heresy era list.