When I flip a structure, the absolute stereochemistry is not preserved.
ChemDraw is behaving as designed. The flip command is designed to be graphical, so it is flipping the structure. If you want to preserve the stereochemistry, use the "Rotate 180 degrees Horizontal" or "Rotate 180 degrees Vertical" option in the Object menu.
In versions of ChemDraw prior to 9.0, select the structure, hold own the Alt key, then click (and hold) on the Object menu. Now instead of "Flip Horizontal" or "Flip Vertical" it should say "Rotate 180 degrees Horizontal" and "Rotate 180 degrees Vertical".