I don't think you need the second file (model). You can do all of this in one run. Refer to the "hot sustained" discussion in the Technical Reference Manual.

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My next question is, if the support is removed for the thermal analysis, would this yield overly conservative results? Or would they be severly underestimated?
Neither/Both - I think it depends on the specific model being analyzed.
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Regards,
Richard Ay - Consultant