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Allegiance is about the keywords rather than the subfaction/book they're in (although those often align). Chaos in particular tends to differentiate by god and racial keywords (for instance, some Battleline units are unlocked by keeping to Mortal and Nurgle keywords).
Long story short, I don't think you'd lose much by taking Archaon, but it depends on the rest of your army. If you mostly have Skaven Moulder and throw Archaon in, you won't keep the Moulder allegiance, but you'll still have the Chaos allegiance (because everything in the army has the Chaos keyword). If you have a Mortal Nurgle army, however, you're good... Archaon has both keywords.
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