After you file

Dear all:

 I have an unresolved problem with IRS. I have been trying to reach out  since 2 months, but rarely been successful to have an agent to talk over phone. I sent my paper tax return and ITIN application for my wife and my child in Feb 12, they processed my tax return and deposited my refund in June 28, but never issued ITIN notices for my dependents. I have been waiting for very long and still see no sign of any help. I even reached out to IRS taxpayer advocate service over phone, they all are suggesting me to file a new ITIN application. Can we file new application as they have already processed my married-joint tax return? they have amended and adjusted my refund higher than I was expecting. They wouldn't process my return if they hadn't my dependents ITIN assigned. They said they don't have ITIN information in their system every time I called to a live agent on phone. Please guide me.