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In case this isn't clear-- you don't "get the chance" to complete Battle Squares, if you left/finished the Temple without doing so. But you can "take" the chance, if you want it.
Battle Squares is completely optional, except for the three battles of rank 1, level 1, which you must do to complete the Temple.
So if you left the Temple without completing it, it does not matter-- unless you want to complete it. In that case, you may walk back to the Temple (you cannot go there via the World Map, but you can retrace your steps from the Wandering Village or wherever to the map exit where you entered Chapter 3), and re-enter the Temple, go to the Battle Squares room and complete BS.
However, once you get onto Oswald's ship at the end of Chapter 4, you can no longer walk back to the Temple, thus cannot complete BS. As Nightowl2 says, the next time you see the Temple, BS is no longer functional (and you have other things on your mind anyway).
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