Hum, I've read about both methods, clearing the contents from the reservoir as much as possible first should help, I've been lazy and never flushed through the ABS block, and I'd be very annoyed if doing that with 4 clear lines caused dirty/old fluid to get into these 4 clear lines!
I'd guess a compromise that could work is to clear the reservoir content out initially by drawing as much as possible from the reservoir, then clearing the shortest line, then run the ABS pump etc which means drawing some fluid from all 4 lines again, then probably dumping the usual quantity of fluid from each of the 4 lines starting at the longest and ending with the shortest?