Can an ability track a card across multiple zones?
Objects that move from one zone to another become a completely new object.


  400.7. An object that moves from one zone to another becomes a new object with no memory of, or relation to, its previous existence. There are eight exceptions to this rule:


Rule 400.7h is an exception to 400.7. This is the rule that allows Jace's -3 ability to keep track of cards that you cast from the graveyard.


  400.7h If an effect causes an object to move to a public zone, other parts of that effect can find that object. If the cost of a spell or ability causes an object to move to a public zone, that spell or ability’s effects can find that object.


As soon as the card moves to any other zone, rule 400.7h no longer applies, and Jace's ability loses track of it. If you cast Walk the Aeons after that, it will go to the graveyard like normal.

As another user pointed out, this is also the most logical outcome. The game has no way to tell in all situations if the second Walk the Aeons is the same physical card as the first one.