So if I have this correct:
1. Some years ago, you filed an application, your ex filed a response seeking unsupervised time.
2. Orders were made that the children live with you and spend supervised time with your ex.
3. Some years later, the children stopped spending time with your ex.
4. In response to (3), your ex filed an Amended Response seeking final orders and interim orders both seeking to have the children reside with him.
5. You filed an application to have the Amended Response dismissed.
6. The Court (for reasons you have not explained) has ordered that your ex amend his Amended Response.
You are concerned that if your ex amends his Amended Response (which he has been ordered to do) he may defeat your application to have the Amended Response dismissed, because the amendments may cure the defects that you are relying on.
None of that has anything to do with what he should call his amended Amended Response. You need to focus on the substantive content of the documents, not whatever title is put on them.
I don't know why the judge has ordered your ex to amend his Amended Response, so I can't comment on whether such amendments may defeat your application for dismissal, whether the judge intended to give him an opportunity to fix the defects or anything else.
If the judge has ordered your ex to amend his Amended Response, then your ex is entitled (and indeed, required) to do so. Trying to keep the first Amended Response "in play" after the judge has ordered that it be amended appears to be a pointless waste of energy.
Well, the reasons he gives in his amended response to apply for residence, the only matter left outstanding, were dismissed in a previous hearing!