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Did the imaging check his neck?
You are right, FCE is not progressive. It should not get worse.
FCE also should not still hurt 2 months later. At most it hurts a couple of days or so.
All I can think is, it does not sound like FCE.
One condition that is sometimes seen in boxers is Wobbler Syndrome or Wobblers Syndrome. If it was that, I think it should show in the cervical imaging.
I have not heard of a problem worsening due to acupuncture. However, I can imagine a situation where a dog had a sore neck with instability in the vertebrae of the neck, and it got worse during a drive to and from the vet, or being lifted out of the car and back in, or onto the examining table and back off, or something like that.
I do not know what to suggest at all, because you already saw a specialist. I think you urgently need to talk to the specialist again.
Ask them if they could re-examine the cervical imaging and see if anything might have been missed. Or ask if they can get another vet in the practice to look at it and see if s/he interprets it the same way. Also, ask them if they think the imaging produced good images. I once had a cardiac ultrasound that was expensive, but in the end the report from it said essentially "lousy images" in several different ways of phrasing it. In spite of what I paid for it, it produced little useful information. I don't know if you ever get poor imaging from MRIs, hopefully not, but I would ask just to be sure.
I believe they will agree with you, these symptoms you describe do not sound like FCE.
Go ahead and be the squeaky wheel. Go ahead and advocate for your dog. I think it is your best option right now. Talk to them again. If nothing else, it sounds like he needs pain meds or a muscle relaxer or something. I'm so sorry you spent so much money and are still in this situation. Please post back what you find out.
You shouldn't blame yourself, because it is totally understandable that you would want another big dog after your experience, and you had no reason to keep them separate because he seemed fine. Teenaged dogs (and cats) can be full of energy and not know when to stop.
I really think if it was my dog, I would absolutely want him on some kind of anti-inflammatory (like prednisone) to see if you can get any improvement. Also, if it was my dog I would ask about a muscle relaxer. If you've ever had a sore neck, the first thing you want is a muscle relaxer. Ask them "What could it hurt???"
You said they saw something compressing his neck in one image but then they shrugged it off and decided it was nothing. I wonder if doing additional imaging focusing on that same spot might be helpful, so you can take a second look and be more sure about it.
Don't take 'no' for an answer. They don't understand how important this is to you and your family, to help this dog.
Right now while he is lying down, do you have malewraps for him to keep him dry? A malewrap is also called a belly band or a male doggy diaper. It's a wide belt that goes around the waist and fastens with velcro. You put an absorbent pad (like Poise or another adult incontinence pad) in it and change as needed. It is extremely important to keep his skin dry while he is laid up. If he lies in wet bedding, he can quickly get a urine burn on his hip and they are easier to prevent than to treat.
If he still has a good appetite, that is fantastic. He's 4 years old, young and strong. I think you need to really go to bat for him. Tell them he appears worse because now he can't walk at all, and furthermore he seems painful, and you know this isn't how an FCE goes.
Actually, if you aren't getting anywhere, something else you could try is to ask elsewhere. You did what anyone would do if they had the money. You went to a specialist. But if you are getting totally nowhere with the specialist, and if you know another vet who will at least listen to you, talk to them. Tell them you did the tests, they said they couldn't find anything, they decided to call it FCE, but you know that what you are seeing does not match FCE and your dog needs help. Maybe your regular vet would consider treating him based on symptoms. Or maybe he will know of another place to refer him to.
I have had 2 unfortunate experiences with imaging here. In the first case they missed the problem completely. In the other case they weren't sure, and based on my previous bad experience I wasn't going to trust them, so I decided to have my pet treated by our regular vet and that turned out to be a good decision.
The other thing you might do is, ask your regular vet if s/he knows whether the equipment in use at the specialty place you went to is top notch. Here where I am there is a different specialty practice 90 minutes away that has the latest and best equipment for imaging. I've decided next time I need imaging, it will be worth the drive. So perhaps your regular vet knows of another practice within driving distance that happens to have newer equipment that might give better results.
I am not a vet and I have no idea what kind of equipment or expertise you have available at the place you already took him to or anywhere else. I'm just trying to think of alternatives since you still don't have the information and treatment you need. You and your dog deserve to get to the bottom of this!