I had the exact same problem of uneven string volume after sanding the underside of the nut to lower the action on an Ibanez.
I glued a square of fine sandpaper to a spare 6 inch wall tile and gently sanded it, just enough to remove the bare minimum of material.
Checked it repeatedly by holding the nut to a straight edge and shining light through until it was absolutely flat.
Only removed the burrs on the edges of the nut, so the contact area was flat and had as much contact with the UST as possible.
It worked a treat, string balance was spot on. Clever old me
