If I understand you correctly you are using the pet palette option to mirror. This is a standard element edit that is generally applied to all elements. Skylights, however, are different. The rule with skylights is that they will always orientate themselves with the slope of the roof. So even if you apply a mirror rotate or even a simple rotate to them, they will always correct themselves. You can't even change the angle of them in the Skylight Settings dialog.
Good luck with your ArchiCAD mastering.
Cheers,
Link.