Certain high frequencies were sometimes boosted on CDs to counteract the loss of high frequencies that would occur with older CD players during the digital to analog conversion process in early D/A converter circuitry present in CD players. A pre-emphasis flag would indicate that this process had been performed on the CD and those CD players with de-emphasis circuitry would act accordingly. As far as I know, this is ignored by all modern CD players and DACs. It is just an option in CD mastering software, because it is part of the Red Book standard.

Stu