So sorry to read your post.
First, to answer your questions about BCG. If you look at the threads at the top of the topic "Non-invasive bladde cancer" you will find LOTS on BCG. Also, if you use the "Search Forum" function at the very top of this page, you will discover much more.
BCG is instilled directly into the bladder where its purpose is to kick up the immune system to fight the cancer. If your cancer is indeed superficial (ie, still limited to the bladder lining) there is no need for systemic chemothereapy.
Your urologist's description of the side effects is spot-on...some burning with urination and fatigue. The side effects do increase as the treatments progress...this indicates that they are working and the body is reacting.
I am somewhat surprised that your urologist did not biopsy any muscle tissue. Many urologists follow the current "standard of care" and do a second biopsy after the first has healed to be sure that they had muscle present. Bladder cancer is very often understaged and a second biopsy, when the urologist is surer of where the problem exits and can get more accurate sampling, is really a good idea.
I would strongly suggest that you get a second opinion on your case at a center that sees LOTS of bladder cancer, if you have not already done so. Your case is not typical and you have additional risk factors (Lynch Syndrome) that make it critical that you get the very best of diagnosis and care. Depending upon where you live, such places as MD Anderson in Texas or Memorial Sloan Kettering in NYC, Johns Hopkins in Baltimore, USC in Los Angeles. If you let us know where you are located geographically, others may have suggestions for you.
As you know, CIS is high grade and nothing to fool around with, and the Lynch Syndrome puts you at greater risk for recurrences.
Best of luck to you, and please let us know how this goes.
Sara Anne