Brain lesions are obviously a serious concern. Discussing treatment and prognosis with an experienced neurologist
) is a must.
In general, the ability of a brain lesion to disappear or just shrink depends on the what the lesion is. Infections, tumors or benign masses can all involve the brain. For example, a tumor will likely remain without the appropriate treatment and/or surgery. A benign mass may never resolve, however these can often be removed fully by surgery. As for infections, they can often be completely cleared with the appropriate treatment. One important consideration is that some infections can form into an abscess, which is a ball of infection that cannot resolve without surgical drainage. That being said, even if a lesion remains, it may cause no further symptoms.
Its unclear what exactly your brain lesion is and therefore difficult to say what will happen. While Lyme disease can often have neurological symptoms (such as causing nerve damage or even meningitis), it would be unusual for the disease itself to cause a brain lesion. It is possible that another type of brain lesion was found when brain imaging was done during your Lyme's disease course.
Discussing the nature of your brain lesions, the treatment and the prognosis with your primary doctor and neurologist is important. If you are very concerned you could also discuss your case with neurosurgeon