My sister has probable endometriosis, chronic sinus congestion, tonsil stones, atrophy in one eye, now blood and protein in urine. what could be the cause?

Unrelated: Don't look for a single cause. Endometriosis is extremely common, as are sinus troubles. A person can learn to remove their own tonsilloliths. Blood and protein in the urine in a woman are often contaminants but a cause should be sought. It's a waste of time to try to connect these. I'm glad you care for her and trust these concerns can all be addressed. Best wishes.