A recent study has suggested that HRT may increase the risk of mild to moderate lupus 'flares'. HRT should only be used for short periods and should be avoided in patients with a risk of blood clots, and especially if they have antiphospholipid (sticky blood) antibodies. Some patients find alternative treatments useful but there have been no clinical trials in this area.
As you suffer from migraines it may be advisable to be tested for "sticky blood", as migraines are a major feature of this condition. The blood tests required are the Lupus Anticoagulant and the Anticardiolipin antibody.