If that action step is interactive when run from the action palette it will also be interactive in a batch run. How was that add 3D layer from a file step created in the action? Was it a straight recording or a insert menu item. I would think the straight recording would just use the same file always and not be interactive where the insert menu item would be interactive where you would select the file and then how the new layer is done. I don't use the 3D feature of Photoshop only played with it a bit so I know nothing about "Add 3d Layer from File....".
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