When the structure flips horizontal and vertical the stereochemistry of structure also changes from S to R, and vice versa.

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, select the structure, hold on the Alt key, then click (and hold) on the Object menu. and then select either Flip Horizontal or Flip Vertical.