I think you are asking about emptying the system then refilling it vs bleeding new fluid through system as you drain the old fluid. While emptying completely and then refilling is typically ideal, a good bleed can accomplish virtually the same amount of contaminant removal.
Don't worry about it mixing. First, suck out all the dirty fluid you can from the reservoir and then refill it with fresh fluid. Make sure you bleed enough to get nice fresh fluid coming out the bleeder valve. You should have plenty of fluid to do this since you got the extra bottle.
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