Coop changes have proven stressful for my girls, and they all reacted to the changes in different ways. Sounds like your girl is stressed and fearful, and she is associating you with the changes to her home.
I understand maintaining the pecking order, etc. ~ but unless I encounter real, long-term, deep-seated aggression in an animal I prefer to play the role of She Who Is The Source of All That Is Good. I hand feed my girls so they know who brings the good stuff, I talk to them and interact with them daily, I handle them gently (and often) and I try to maintain an atmosphere that feels safe and quiet to the critters. I do not want an animal to cringe or feel stressed when I enter the pen; I prefer hens waddling over to see what I'm doing. This trust gets them through the hard times when I have to do things that are not so pleasant for them, like medical care, etc.
When I have had fearful animals who show aggression I pay more attention to those. How about playing "Who's the Baby" ~ firmly but gently holding the recalcitrant hen on your lap, petting and talking quietly, and maybe slipping her a few nice grapes until she associates you with something good. Only offering treats at odd intervals prevents hard-core behavioral conditioning on the food expectation.
Also with these fearful animals, when I get the sense that one is thinking about taking a swipe at me, I place all my attention on him/her ("Ah, you want my attention? You want to be the baby?") That individual gets picked up and loved on or at least petted or spoken to directly until the aggression subsides. The critters who do not enjoy this will not wish to have my "attention!"
Good luck!
Jen in TN - She Who Is The Source of All That Is Good
