Hi Glynes,
Might be worth having a look at the judgement in the Supreme Court case Mangoola Coal Operations Pty Ltd v Muswellbrook
Shire Council on the Case Law page. This found that rates are protected by the Recovery of Imposts Act, which means Council would not be required to refund rates paid voluntarily more than 12 months ago. In your case, even if the property was rightly non-rateable in that previous period.
It’s probably up to Council how you wish to proceed, but this is really good precedent if you don’t want give the rates back in those past years.
Cheers
Ian