Blizzard haven't given a detailed enough explanation of the system to be able to say for sure, but I doubt there is a separate counter of BLP for each spec. If that were the case, then it would be possible to have a higher chance to get a legendary on a spec which you have a lot of legendaries on, than a spec which you less legendaries on, depending on how much time you spent collecting BLP for each spec, which would lead to a contradiction (since Blizzard has stated that you have a higher chance to get legendaries on a spec which you do not have many legendaries on).
What would be more consistent with what Blizzard has stated would be if you simply had one quantity for BLP for your character, and this affected the drop chance for all your specs. The thing that differs between specs would be the base drop chance of getting a legendary (the drop chance before being affected by BLP). This would also be a lot less complicated way to code it, since it would simply use the same variables as before, rather than creating a whole set of new ones to track BLP for each spec separately.
In other words, in my opinion, yes, you have reset your BLP counter, and need to accrue it again before you have a decent chance to get any legendary. The positive side to your situation is that swapping to Windwalker made it easier for you to get that legendary, so now you have more legendaries (on average) than you would have had if you had stayed on BrM the whole time.