Hello and thank you for your question.
If the loan to you and your estranged wife is documented and can clearly be demonstrated to be a loan not a gift then the loan will be repayable by you and your estranged wife, but unless the loan was expressed to be secured against the property there is no entitlement for them to lodge a caveat on the property (which I suspect is roughly the equivalent to the lien they are contemplating - the law relating to liens in Australia is quite different from that in the US so hence the terminology is different).
If the loan is not clearly a loan but rather the court forms the view it was actually a gift which is only now, on separation, being described as a loan, the courts will not order it be paid back, but in such a case will generally regard any such gift from a parent to a married couple, as being a financial contribution of the party whose parents contributed, so that the gift should at least benefit you to some extent as reflecting your contribution, and which therefore will potentially entitle you to a greater share of the asset pool upon a family law property settlement or judgment, (though whether it benefits you to the extent of the 'gift' only a fully briefed lawyer can advise on).
If there is no net equity in the house, the money is still repayable as a loan (just because the asset the loan was used to purchase proves to have no net worth, does not excuse the borrow from repaying their loan) and is still taken as a contribution on your part, if the court determines it a gift.
It is only if you and your estranged wife were to become bankrupt that the obligation to repay the loan would be reduced to what could be recovered out of your assets, and any shortfall would simply be unrecoverable.
I trust the above assists your understanding.
Good luck and PLEASE RATE MY ANSWER.