Solved the problem. In the subtransforms <transform ... > header, set "create" to equal 'existing'. By default if it's not specified it makes it mean 'new'.

Link to the documentation: https://docs.intersystems.com/latest/csp/docbook/DocBook.UI.Page.cls?KEY...

Example:

<transform sourceClass='EnsLib.HL7.Segment' targetClass='EnsLib.HL7.Segment' sourceDocType='2.4:PRD' targetDocType='2.4:PV1' create='existing' language='objectscript' >