Anything downstream of the furtherest upstream connection that is disconnected will have air bubbles that need to be pushed through it. As long as a connection is not undone (and air is not introduced) upstream of the ABS unit, you should be fine. Brake fluid flows right through #1 & 2 all the time, and bleeding will or course force fresh fluid through them. In other words, all fluid flowing from the master cylinder to the calipers will only be flowing through those lines.
In that case, a standard bleed should take care of it. I have 2 fresh bottles and may just flush with 2 liters for completeness.