Are you bleeding or exchanging? If you have air in the system, I could see it mattering. But, if it's just a fluid change, how could it matter, other than maybe you waste some fluid?
I'm not sure how the fluid inside the ABS pump could go bad, it's a long ways from either end. Any moisture in that fluid would have had to migrate slowly to it--and if it could migrate to it, then I can migrate away from it, by the same mechanism. IMO, change the fluid in the master, then pull what can be through the lines, and call it a day.