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Maybe you can use the ##class(%XML.Reader).Correlate method.
If you wrote the transform, then you presumably know what it does. Our transforms have a Canonicalize template. But, I don't think we should be removing an element. My guess is your template isn't really being called.
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SDA may be too large to instantiate a Container object. Instead, use ##class(HS.SDA3.Container).InitializeXMLParse and ##class(HS.SDA3.Container).GetNextSDA to instantiate each streamlet.