It seems the counter goes up everytime you pick up resources regardless if they were previously picked up, I'm saying this because the achievement popped for me while taking all the junk in my workbench and transfering it again back and forth. Not sure if this is a valid way of obtaining this achievemnt but surely you'll want to try it once you have a good amount of junk and resources stored in your settlement.
EDIT: This video shows how to do it and further confirms this method is in fact valid, props to Reabo for recording it.