Estrogen does tend to affect migraines, so it may be nothing more than that. Migraines, if they don't have a scarier cause, are basically sensory phantoms. They don't do any damage other than the pain itself.
I've had migraines for 11 years, and I knew going on HRT might be an... interesting experience. I've been through a few rough patches, but they are mostly under control. Try not to think of it as hopeless, and wait till you've talked to the neurologist. If there isn't something serious causing the migraines then you could be fine to continue. You'd just need something to treat the migraines.
Really hope it works out,
Sarah