The bacteria, if not promptly destroyed, become encapsulated in various areas of the body where biofilms protect them from destruction. Thus, with many bacterial infections (tb being a case in point) you only end up "in remission" after treatment, and the bacteria reproduce years down the line when the immune system beciomes weak.
The symptoms that you describe may have nothing to do with Lyme disease. Lots of people get these types of symptoms without having been bitten by an infected tick (this is how Lyme's Disease is transmitted).
Make an appointment with your doctor to check out your knee and calf problems. Knee pain can be from osteoarthritis which is a degenerative bone disease. You doctor may refer you to get an xray done to see what is going on with your knees.
The calf pain should also be investigated to rule out blood clots. It may be that it is a muscle problem and nothing to worry about, but if the doctor has not checked it out, then it would be a good idea for you to get than done. A blood test called a Doppler test will show if you do have any problems that need medical attention.
Sometimes the pain that you experience down the leg can be referred from the spine or knees.