My sister has small kidneys and it really hurts her some nights what could she do to stop it?

Needs more testing. Small kidneys are not necessarely painful. It is possible that she has reflux nephropathy in which case urine infections could cause kidney pain usually accopanied by fever and chills. Small kidneys are either maldeveloped or chronically damaged by inflammation or infection or trouble with circulation. They are associated with kidney failure of different degrees.