The Root of the Behavior
Dental issues like broken teeth or infections in the mouth could be causing this pain as well. Bones and other hard chewing toys often cause the cracking and breaking of teeth which could be putting your dog into a great amount of pain. Assuming it is just broken teeth, this can be less concerning than the alternative. An infection in the mouth can spread to other parts of the body and risk your dog's life and well-being. However, cracked or broken teeth can eventually lead to infection and still should be treated. Abnormal swelling in the throat could cause pain to your dog during or just after eating. The cause of the swelling could come from a thousand different places, ranging from cancer to just irritation. Keeping an eye on the swelling is important, and if it persists or gets any worse, you should reach out to your vet as soon as possible and treat the root cause of the swelling.
Encouraging the Behavior
A big step is to get them off bones, or at least reduce their quantity of bones. Although your dog loves them, and they are advertised as the best thing that ever happened to canines, they can cause a lot of harm with relatively few benefits. Bones fracture teeth, and can splinter and rip apart the stomach and throat. Transitioning them to a chew toy instead can make a large difference when it comes to long term canine health. Chew toys are usually designed to be much safer then your typical bone. They are soft and immune to splintering into sharp fragments.