Yes, lyme spirochetes as well as the toxins they produce do live in the tissues and bones and can cause damage. One must remember that lyme spirochetes or bacteria's (any variety of them) do have a life span and once dead (either by natural botanicals or chemicals) do leave toxins in the body including ammonia.
That's the reason why heavy detoxing is utmost important. To rid one's body of these toxins can prevent damage and chronic symptoms.
Have you read this article below about Toxins? Very interesting.