B vitamins are water-soluble. Anything extra will be flushed out with your pee. Everything I've read, 50-100 mg of B6 should do the trick.
Vitamin B6 isn't progesterone. It's thought to lower your prolactin levels, thus increasing your progesterone levels. I imagine it would take a few months to see a difference in your LP. So you should be just fine. An endometrial biopsy would be more accurate in diagnosing a LPD though.