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Hmm, well, I say it counts as canon as much as Storm of chaos does.
Was it retconned? Yes. Does that make the events that happened in that storyline any less relevant? (Like a secret being revealed, a character doing a amazing feat, etc.) No.
It's best to think of them as alternate timelines where, though it's occurring in the same universe, there are different paths taken that make a new outcome.
So in essence they basically are canon.
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