"Western blot analysis can detect one protein in a mixture of any number of proteins while giving you information about
the size of the protein. It does not matter whether the protein has been synthesized in vivo or in vitro. This method is, however, dependent on the use of a high-quality antibody directed against a desired protein. ...'
askabiologist.asu.edu/western-blottingIn order to have a band on the Western Blot turn positive, there must be an antibody produced. Lyme and Bartonella both inhibit the immune system from producing antibodies to the bacteria, can create biofilms (as you have indicated) so that the immune system can't interact with it or morph to no longer have a cell wall for the immune system to react to.
A much better way to tell how well you are doing is by symptom relief and then time. Stress is usually what will "test" a person's recovery.