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Don't worry about rubbers as long as you're not using any petroleum-based cleaners. Brake-fluids of all types contains conditioners and lube for rubbers.
You really want to use 100% isopropyl alcohol or denatured alcohol to clean out brake system before going to DOT-5. Alcohol dissolves glycol-based DOT-3/4 fluids to thoroughly clean system and not leave any trace compounds behind that'll contaminate fresh DOT-5.
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