Congratulations on getting to day 28 of your water only fast. Great job.
Dark urine only means that your body is still detoxing. It is good thing. When it is really clear then I would worry, not with dark or orange color urine.
During a fast the muscle never gets eaten unless you are in a starvation mode. You are really fasting so no way your muscles are going to be affected. If you fast after all your reserves are consumed then your lean muscle will go first. But by that time you will feel true hunger.
Don't worry, continue fasting. Do take care in listening to your body after 30 days.