FYI, the idea that active infection continues to exist in hiding within the body is a fringe theory.
The linked article talks about one of the current theories for why some patients have persistent symptoms after the infection is treated. The theory involves certain components of the past infection lodging themselves in the liver where they persist and can cause symptoms.
This is a difficult topic because some alternative Lyme treatment providers will tell patients they have a persistent infection and then subject them to years of high-dose antibiotics with no scientific basis, which can create a separate set of problems without addressing anything.