When it comes to the recovery of wages, and in particular this matter where such a period has transpired, a company can soon face a BIG problem.
Firstly, there is the simple act of law that looks at 'Custom and Practice', and the knowledge of how the payments were origionally set up. There can be a problem recovering from something that historically has been approved by virtue of entering in the times into a sytem setting the practice, all the way to if the company was aware that the hours reduced, initated the reduction, but did nothing to change the wages as a result, particulartiy if its not in writing, then you could very well be seing good buy to the over payment.
Then if this is not the case, you will then struggle to offset any of his current wages being paid to him (or her) as under the fair work act, section 323, the worker MUST be paid for all work performed, and this is where the action gets tougher on the company.
This is loosly termed 'off setting' or to set off an overpayment against an underpayment if you dont pay wages in accord with section 323, unfortunatly, you will loose here as well. Many cases I recomend would be 'Polliti vs Ecob (1989) 91 ALR 381, Logan v Otis Elivator Co PtyLtd [1999] 94
IR 218, this later one the Court ruled
'If an employer does not designate or appropriate the excess (over payment), or any part of it, to a particular obligatin owed by the employer to the employee, it is not open to the employer to later change that situation by asking the Court to retrospectivly designate between various elements [of an award obligation]...'
Further preventing this from moccuring is the matter Foster v Faulkhead Nominees Pty Ltd [2005] SAIRC where the court provided 'An over payment made for wages due in one period of time, cannot be set-off against monies payable for wages due for a later distinct period'.
You have a tough road ahead, and its not a matter that the new FWAct has put business back 50 years, but that business has an obligation to ensure is processes and practices conform to the law.
Good luck