Textliner,
Do you have information on what might be causing the shorts? The first step would be to determine if it is a direct electrical short or if it is some electrolytic coupling. More testing to confirm is recommended as suggested above, hopefully you use a competent CP consultant who knows how to complete various tests. If it is not a direct short, you can probably fill the casing with dielectric inhibitor; you may also want to install new seals. If it is direct metal contact, you wouldn't have much option but to physically clear the short. You may also want to check and see if the casings are shorted through the test post wires and not the pipe. As far as taking the line out of service, I don't know your procedures but many operators allow excavations with a reduced pressure.