DH was unable to get one of his payment summaries when we had to catch him up on SEVEN years worth of tax a couple of years back. the accountant simply put in a nil return - so they took whatever amount of tax he'd paid that year and didn't allow him to claim it back - as Astrid said, ATO should have a record of the amount you were paid...
c'link wise you can request a copy of your payment summary to be reissued
FWIW - because we got the accountant to do the return, we didn't end up having any penalties for all the previous years - no idea why though...
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