Must be the season. I recently got a Super Commander, worse yet, in Black Cerakote from Emerson. I am starting to add Wicked Edge sharpening to my skillset and service offerings - I am starting a small business, don't ask why - and after sharpening a handful of "practice" blades with no problem, decided to work on the Emmie. Effed it up way worse than yours; I went from pristine to having all kinds of scratches - the clamps slipped, left trench marks; I overshot angles, left channels; it's a horror show. I'm so torn: a large part of me wants to smash the knife with a sledge in the driveway, so I never have to see it again, and see how badly I effed it. I've actually had it sitting on a towel in the drive with a sledge in my hands...
I swear the knife has bad karma. I've never, never, done so much damage to a knife - and I started sharpening freehand when I was 12 or 13. Even reprofiling on a power bench grinder when I was 15 I didn't make this kind of mistake. Really rookie, really ugly, really makes me feel like a complete and total horse's arse.
I'm going to continue to use it for a bit. I'm working on putting a broader secondary edge that is mirror polished on it; so I get practice remounting the knife in the sharpener to match angles precisely. I contacted Josh at REK; he suggested that a stonewash could be done fairly reasonably, and that would probably take care of the scratches. I'm sure that he could also come up with a reasonable way to put an entire Cerakoting on the blade. I don't have the cash for it now, it will have to wait - but Josh is a high-order Wizard, I've had him do work for me before. I would have him do the work before I ever contacted Emerson, btw.
I had previously put a new titanium pivot screw and standoffs on the knife. The pivot screw was blue; the first time Simichrome touched it, all anodizing came off in 2 seconds, with one wipe of the cloth. I called Emerson about their hardware - bought the stuff off their site - and was literally told that my pivot screw was still blue, and that I just couldn't see. But, the guy said, if I'm going to raise so much fuss, he'll send me a new one, maybe I'll like that one better. But, he warned me, what I described was literally impossible, and couldn't be happening.
Good luck with your Emmie. If I'm in a bad enough frame of mind someday, I'll post pics of my mess.