If a Favored Class Alternative choice gives you more uses of a class ability a day but a variant takes this class ability away and gives you a different one do you lose the extra uses or do they now count for the new ability?
I haven't found anything so I'm assuming you lose the bonus. Am I missing something?
But remember that u can always pick hp or a skill point if you play a variant class, as the variant is chosen at level 1, so you wouldnt really lose the bonus, just dont take it.