Will a newly recruited Aztec swordsman have the special ability of the Eagle warrior? Should I make a huge batch early on?
The answer is NO.
From this wiki page.
Unfortunately, Eagle Warrior's ability is lost when it upgrades to a Swordsman.
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^ any units Unique Ability IS lost when upgrading to a higher tier unit in Civ VI. Of course, you do not lose any promotions bonuses, exp or levels. In previous games, upgrading a Chu-Ko-Nu (for example) into another unit still let the unit keep it's fire twice ability, which was very OP. – CoqPwner Dec 13 '16 at 20:07
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In Civ5, unique abilities were implemented as special promotions assigned by the game engine when training that unit. – David Harkness Dec 19 '16 at 3:24