you don't have to flush anything when changing over to silicone brake fluid. just remove as much fluid from the master as you can and fill with silicone fluid. then bleed brakes until the silicone fluid flows out of the bleeders, silicone brake fluid is blue so you can easily see it flow out. i like to bleed one more time to remove any excess old fluid that may hide in the system.
don't worry about the 2 different types of fluid in your system. if there is any old fluid in your system it will not effect the silicone fluid. it may lower the boiling point and eat the paint off, but your brakes will work just fine.

remember silicone fluid retains air like the old stuff holds moisture. so if the bottle was shaken while on the shelf it could be full of air. if that happened and you don't remove the air your pedal will never get hard. one way to prevent this is to leave the silicone brake fluid out in the sun for a couple hours with the cap off to boil out the air trapped in the bottle or better yet place the bottle in boiling watter for 10 min.