That’s actually a frustratingly hard and time-consuming fix.
The ‘part’ in EAGLE - the electronics CAD software that generates the board - that represents the header is, in fact, a part that represents an entire mobile B Pi - so it includes both the header and the three mounting holes and markers for the pi’s outline. Flipping that piece of silkscreen would involve… redesigning and replacing the part in its entirety.
If I were to suggest a fix, it would be adding text saying “place header on underside” along the top of that outline.