It's an old wive's tale that you have to completely flush conventional brake fluid out of a system before putting DOT 5 silicon fluid in. I used to be an engineer for Raybestos, and no one there ever said there would be an issue if there was a little Dot3/4 in the system when you added silicon fluid. In fact, I've generally used Dot 5 as assembly fluid when rebuilding master cylinders and wheel cylinders, regardless of whether the cylinder is going in a vehicle that uses conventional or silicon brake fluid. Never had an issue, from a chemical standpoint, not sure how an issue could occur. By far the biggest problem with brake systems is when the seals are exposed to anything petroleum based, EPDM and SBR rubber used in brake cylinders swells up and fails when exposed to petroleum based fluids, those compounds get along just fine with Dot 3/4 and silicon and mixing them doesn't alter anything (exceptions being Rolls Royces and light aircraft that use petroleum based brake fluid!)
When I've changed over fluids in a system, I open the bleeders and let the fluid run out while adding Dot 5 to the master cylinder. I keep doing that until the fluid running out of the bleeders is purple.
Whatever you do, don't flush a brake system using alcohol. That will damage the seals and cause problems!
