The first 3D model published to the workflow (with process step MergePublishedFile configured) creates a composite 3D document, the first version of the document, and copies the 3D model from the published 3D model.
Subsequent publishing of the 3D models into the same workflow result in the following actions:
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Create a new version of the composite 3D document.
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Merge the newly published 3D model into the existing composite 3D model.
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Attach the merged composite 3D model to the new version of the composite 3D document.