I'm not sure if this is intentional or not. When you load a pre-baked opacity texture into ddo, it doesn't seem to carry through to 3do. You have to import the texture again in 3do, and you have to do this each time you load the project. Is there a way around this? Does the pre-baked opacity option just not work at all, or does it get incorporated when you export your textures at the end?
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Just move the pre-baked texture to the very top of the layer stack and force-refresh. Should fix it right up.