Generally, you don't have to duplicate an account on Form 8938 that was also reported on Form 3520. This would apply primarily when the form is used to report a foreign trust (another use of the form aside from reporting the foreign gift/inheritance).
Include the amount transferred to your Australian checking account on Form 8938. There is no tax associated with your balance so there will not be any negative consequence to including the amount.
Since high balances, not final balances, are used on foreign bank account reports it is fairly common that money is "double-counted" due to transfers between accounts owned by the same taxpayer. It is not uncommon that the form appears to overstate a taxpayer's financial position on these reports annually.
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