Rule number 1... If separation is on the cards, make sure all joint accounts require both parties to personally attend the bank and sign off on withdrawals and transfers.. Either that or withdraw 50% into an account in your name..
All you can do now is apply for a property settlement if you havn't already and be diligent in making sure that the proper process of full and frank disclosure is adhered to... The court will require actual evidence of loans being made, and if they were made during the relationship, they are a joint liability...
It dosen't matter if there are no funds left, if she is found to have removed joint money without your knowledge or consent, then in most cases where it can not be justified the court will consider it as an add back, meaning that when final orders are made, the add back amount will be counted as money she has already received from her percentage of the division