To flush the brakes if you are replacing with standard flluid just bleed each wheel until you see the fluid run clean. If you are changing over to silicon fluid you pretty much need to disassemble and clean each component with alcohol and flush the lines with alcohol. Brake cleaner will work but don't let it contact any seals. That's why alcohol is better. If you're rebuilding your entire brake system anyway then silicone ain't a bad idea, but to change it just to change it I would say is more of a pain than it's worth. Of course if your master cylinder is leaking enough to corrode surrounding items you probably need a rebuild anyway.
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