Colin ....the last I heard about autophagy is that the cause is maybe a prion (like mad cow disease) . We've had it twice in the aquarium a real*(&#*%$* cos the only thing you can do is euthanise, then strip (& I mean STRIP) the aquarium, chuck out anything you can replace and sterilise the rest. We sterilise by bleaching for a week, then counteracting the bleach for a week, then freshwater (milliQ) in the tank for a week, then reseasoning the tank then rebuilding the rock work, plumbing etc It's a major job but in our experience essential. The one time we didn't go through this procedure we lost a second octi to the disease...it is highly contagious.
Big Red, I wouldn't panic yet. If she has autophagy she'll eat her other arms very quickly. Our 1st one only lasted a couple of days after the initial symptoms appeared. So keep an eye on her, chances are she's caught it on a rock or something.
J