Hot flushes during menopause may not be due to estrogen deficiency alone.  Run-down adrenals also contribute to hot flushes.  

Also adequate amounts of the adrenal hormone, DHEA, are required for the body to make estrogens (and testosterone).

Natural bio-identical hormone replacement therapy is used in women to reduce menopausal symptoms.  It is also used to prevent cardiovascular disease, osteoporosis and some forms of Altzheimers disease.