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So the Epic Deed Stratagem Strange Echoes lets you swap a C’tan Power for another mid-game.
Two questions about how (if) it interacts with the unique powers.
• Can you use the Stratagem to generate a unique power to replace a generic one
• Can you use the stratagem to generate a generic power to replace a unique one.

The correct answer to both is probably no, but the problem stems from overloading, again.
Specifically, Powers of the C’tan is both the title for the page in the codex and the heading for the list of numbered, generic powers.

Also, it may technically be RAW that the C’tan can’t take any powers because the unit entries say you can take “C’tan powers” but those don’t exist, only “Powers of the C’tan” do. But that’s an aside, please ignore for now.

RAW you can swap unique against and general powers, and vice versa. HIWPI, only unique can be replaced by generic. It makes no sense that a transcendent ctan knows the power of the void dragon, or the deceiver knows the power of the nightbringer.

 p5freak wrote:
RAW you can swap unique against and general powers, and vice versa. HIWPI, only unique can be replaced by generic. It makes no sense that a transcendent ctan knows the power of the void dragon, or the deceiver knows the power of the nightbringer.

Could be some Cryptek has decided to see what stuffing two shards in a cosmic blender does. Alternatively it could be a lesser shard without enough personality to manifest as a “proper” Voidbringer (or whoever) bit but can manifest his signature ability if prodded correctly.
Anyway, the point is that making sense fluff-wise only gets you so far. Remember when the Nightbringer and Deceiver were literally the only two (well, three if you include the rumour that the void dragon was still around) C’tan left because they both ate all the others between them? Back before the sundering and the shards everywhere bit was a thing.

Not that I disagree with you necessarily but I’d like some more solid rules backing because fluff is nebulous and mutable.

RAW I think you can, because they messed up by including Powers of the C'tan as both the page title and the table title.

But if you go by RAW then you can just give a normal C'tan the Nightbringer and Deceiver powers at the start of the game anyway since it's the same wording.

You should just assume that Powers of the C'tan (page 68) only refers to the table, because there is no way to actually choose a unique power, it is automatically taken as one of the two powers by the respective unique shard.

From the Codex: Necrons FAQ v1.0:

Q: Can unique C’tan powers be selected for a C’tan Shard unit other than the one specified?

A: No.