We are a job shop as well. While we do not have any of the latest and greatest Haas machines, we do have a Mini Mill from 2006. This thing had, at last count about 6-8 months ago, over 14,000 hours and over 850,000 tool changes. So it has seen a bit of running, to say the least. I have cut everything from mild steel, to 4140 @27-34HRc, to plastic, to brass, to aluminum, to carbide (not something I will ever do again, but that's another story). It will still hold 0.0005" total tolerance day in and day out. No chatter issues either.
Not that it means anything, because I know it will not take the cut (load) that a VF2 will, (we have a 2002 VF2SS as well). Please step back and really think about this logically before you answer the question:
Are you sure that is a ball screw issue?
I ask this because you mention that it only happens on "certain sides" of the part. If the X ball screw was truly wore out, you would have chatter at every X change of direction. Especially since we climb cut, we are always pulling the table with the tool in the same direction the ball screw is trying to push it. Any backlash in there will come out as chatter, digging in, or if the backlash is bad enough, broken tools. The same for the Y axis.
When you change the ball screws and nut, does it fix the problem? When you change the ball screws and nut, do you replace anything else like the bearings in the pillow blocks? If so, have you ever considered changing just the bearings in the pillow blocks? Our swiss screw machine was having problems holding size/shape last year. One of the bearings holding the ball screw went out. Replaced it and all was good.
Just some other things to consider besides the screws. Even though this does not answer your primary question, I hope it helps to at least consider some other possibilities that may be causing your chatter problems.