Academy at Tolaria West's first ability has an "intervening 'if' clause." That means (1) the ability won't trigger at all unless you have no cards in hand as your end step begins, and (2) the ability will do nothing unless you have no cards in hand by the time it resolves.
Academy at Tolaria West
If you discard your hand as a result of rolling {CHAOS}, Academy at Tolaria West's first ability will then trigger at the beginning of your end step (unless you planeswalk or somehow put a card in your hand before then).
A face-up plane card that's turned face down becomes a new object with no relation to its previous existence. In particular, it loses all counters it may have had.
Magic: The Gathering · ™ & © Wizards of the Coast · Illus. James Paick
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