Currently I have recommended to colleagues to use the advanced model template wizard (Tools> Master Template> Master Template Wizard > Advanced) and import the .mit file type. This workflow required 2 projects. One using just the geometry shell and the other as the original working file. This seems to be a way to bring in the new Geometry into VE and maintain the Thermal templates. It is crucial to keep the room names the same to avoid duplicate rooms using this method and change them after the new geometry is brought in to the existing VE model. I would be interested to know if others have a more streamlined workflow currently.
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