File down the rough edges so water flows over it nice and let it go, won't hurt a thing, it is there to hit before the prop so now your prop is more exposed but as far as performance you will never know if it there or not.
The main function of the skeg is to protect your prop. A SkeGGard is a lot cheaper than a new prop and a lot of insurance against sitting in the middle of the lake with a busted prop.
Just like insurance. If nothing happens, you don't need it; but if. . . . . . . .