Hi jasper
Sorry to hear about your ongoing migraines. I would be surprised if 50 mcg patch would override your cycle - doses usually need to be higher than this to achieve suppression of ovulation.
Re blood levels of progesterone - when in your cycle were the blood tests taken? Progesterone is usually measured to determine whether ovulation is occurring and if so whether progesterone levels are sufficient to maintain a pregnancy. In this scenario they are taken sometime during the second half of the cycle - can't remember exactly - but probably around Day 17-22 when they should be at their highest. If they are taken during the first part of your cycle they would be expected to be low - this is normal.
I can't comment on your Day 5 migraine apart from to sympathise because they are so wretched. At this point progesterone levels should be at their lowest, and oestrogen levels should begin to rise. These levels are at their highest about a day or two before ovulation. So if it subsides before ovulation - then surely it cannot be due to high levels
per se - since levels only fall following ovulation

. It sounds like it is due to changing hormone levels in some way - but as you say if you are peri-menopausal they are likely to be variable anyway.
My cyclical migraines always occurred in the week leading up to my period - usually a couple of days before so were either due to the oestrogen dip or progesterone withdrawal symptoms.
Sorry I can't help further and hopefully someone else might be able to suggest what to do?
Hurdity x