I've been wondering, if you transition, hormones, surgery and all, if it changes your scent? Would you become unrecognizable to your pets and have to earn their trust all over again? What if you have a pet that happens to hate human males? Will she hate me if I fully transitioned?

Great question, I can't answer it though! I only crossdress, but my dogs either don't notice or don't care that I change appearance. Scent would be different, but my gut feeling is that it would take more than transition to fool a dog. I know there's a punchline in there somewhere........Tracey

all this the-dog-not-knowing-you-after-transition scenario is possible only if you do transition while your pet isn't around.
if you leave female and come back male after 1 year then yes, your scent might have changed and you'll probably have to make friends with the pet again. if the dog lives with you, then it sees you change gradually and just gets used to it.