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So, if I move my Night Scythe into a position where it can follow the rules of its deepstrike and I drop my Flayed Ones, is it disembarking or does it follow the deepstrike rules?

Do noght scythes have the transport keyword? If yes. Disembark. If no deepstrike.

There aren't generic deepstrike rules, each unit has the full rules for their deepstrike-type mechanism on their datasheet. The flayed ones in built deepstrike ability requires you to be 9" from an enemy, but deploying from a nightscythe with the invasion beams before it moves you only need to be 1" from an enemy.

Expect changes to that in the codex