Sounds very similar to my experience and all the 'is it thrush, is it BV, is it blah etc' that I went through too.
The Vagifem won't affect your migraines, it is local only and will only affect that area. Do use the Ovestin as well, because if you can feel it (ie papercuts), it is in your vulva (usually) and that bit isn't going to be reached very easily by the Vagifem. The vulva and the vagina have separate blood supplies so often need separate treatment. Just put a thin amount of Ovestin on every night after your Vagifem. And use the YES in the mornings. (BTW, I think YES OB is better than YES VM or Sylk
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Don't expect overnight miracles but in about a month you should be feeling fine again. You will always need the Vagifem at least twice a week and the Ovestin as needed though - if you stop, it will come back. Unless you start systemic HRT and that provides you with enough estrogen. (20% of women need both local and systemic HRT.)