Thanks for explaining why the part orientation is important. I can suggest 3 ways to reorient the part around the axis system.

1. The easiest way is to create a new Axis System, and use that for your CFD analysis,

or

2. Use Transformations (Axis-Axis, Translate, Rotate) to reorient the part to the Absolute Axis System. (for your part, Rotate the PartBody 180° about the X-axis)
or

3. Start with a new Part file and rebuild the geometry in the correct orientation.