There are two processes occurring. The first is to save that which is salvageable. The second is to pluck off those that are most bitter, those farthest gone into apostasy, those for whom there is no hope. This is a principle taught in Proverbs 10:24: “The fear of the wicked, it shall come upon him: but the desire of the righteous shall be granted.” There is, of course, an ultimate time when this distinction is made. It is made at this point in the allegory to show that there are those who will not bend to the will of the Lord.
After the section describing the despair of thinking that all was lost, these actions show the continued attempts to save humankind. Note that the image is that the roots may take strength. The root continues to be God’s covenant promises to Israel.