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You'll have to do a complete fluid change Scott and I would run a 1/2litre of brake fluid through each bleed nipple to make sure the water is well flushed out.
As for silicone do you mean silicone fluid or a gel?
The silicone sold here is Dot 5 and is not for modern cars as it has a very low boiling temperature, it is just for older and slower classic cars.
we were doing alot of work on a 2002 golf gti, after a long day and reaching completion we realised that the top student had put coolant in the gearbox