I've always called "Earth-1" Earth Prime. And to me, Earth Prime IS Earth-1. So the numbering system still works.
As for Supergirl, I call her world, Earth-59 since 1959 was the year Supergirl made her debut in the comics.
Think that the major effect of the Flashpoint coming due to barry saving his mother will be to have the earth of Supergirl cease to exist, as it folded into the Flash earth, and for past 5 yeras, Supergirl would have been operating here all along, and both arrow and flash cast know her!