It takes awhile to heal because we need to do more things than "just" killing the bugs.
The bugs actually exist in our bodies in low concentrations. It's their disruption of our immune system that causes inflammation which, in turn, is what drives our symptoms.
Healing requires a holistic approach and others have already mentioned some of the factors that can affect our healing path.
My LLMD was focused only on killing and got me to 90% on abx. He left me on my own to figure everything else out and eventually released me. I plodded my way through herbal protocols and ultimately sought help from a Buhner-recommended herbalist.
And, I continued to address the "system disruptors" in my life that made healing challenging. I consider myself at 99.9% healed (feeling/functioning great with super-minor flares (tingling, etc) here and there while still taking certain herbs).
Most of us have "system disruptors" as described by Dr. Bill Rawls here:
/rawlsmd.com/featured-posts/chronic-immune-dysfunction-lyme-diseaseHow I wish Dr. Rawls' book "Unlocking Lyme" was around when I was first bit. I know my healing journey would have been much shorter.
I have no association with Dr. Rawls and am not trying to sell his book or anything. I continue to mention it on here because I consider it a valuable tool for healing.