You could appeal the magistrate’s decision. That is one way the magistrate might come to understand that his decision was wrong, if the appeal is successful. But then again you have to weigh up the costs.
You should now be asking for both applications to be heard on the same day, then the magistrate has to take into consideration all the evidence from both sides. I am presuming that your application is a temporary one until it can be fully heard in the court.
Besides that, and as far as the magistrate not knowing about your protection order it was the job of your solicitor/barrister to fully acquaint the magistrate with the circumstances of the case. They should have advised the magistrate that the mother’s application was in response to an order issued for your protection. They should also have asked for an order to allow you to return to the house even if the police have to accompany you so you can collect your personal and work items. These orders are rarely refused if explained properly.
In addition to that there is usually a part within the forms that one fills in when you apply for a protection order application that provides for any current/previous orders that are in place. If your ex-partner filled her form in correctly she should have alerted to police/magistrate to your already existing protection order application.
As far as the children’s safety goes you should by now consider having an Initiating Application and affidavit into the Federal Circuit Court seeking sole residency of the children, complete with a “Notice of Risk of Child Abuse” and an accompanying letter to the Registrar explaining the need for an urgent hearing, which would hopefully be granted within a fortnight or so.