"...the phosphate layer..." No such thing. Parkerizing is a coating, not done in layers. Unfortunately, like Dfariswheel says, there's no touch up for parkerizing. However, if the parkerising is black, regular cold bluing can hide the scratch. Brownell's sells a spray on and baked lacquer in assorted colours that might help you.
http://www.brownells.com/aspx/ns/sto...BAKING+LACQUER