I had pretty much what your talking about, only mine was caused by fungus (cleaned it off, glass O.K., but the coating gone where the fungus had been). I removed the rest of the coating, as suggested by Tomosy, with polishing tooth paste (and a whole pack of Q-tips). I took a couple of hours, but the result was perfect. No one could tell anything has ever been wrong by looking at the lens.
However, as Brian says, why bother? Tomosy says an uncoated element is better than one with half the coating gone but gives no reason, and I can't see why. I shot several rolls with the coating half gone, and I can't tell anything from looking at the pictures (and to be quite honest, I can't tell them apart from the later ones wihtout coating, either (but I know which are which from the negative sleeves)).
Perhaps it depends on which surface it's on. I removed it mainly because it annoyed me, I suppose.
Shoot a roll and see if you like the results before you do anything.
(Edit: My coating woes were on the first surface of the second element in a Tessar-type lens.)
