That's good news, really
! Don't be too put off by the puppy's darker coloring: the one thing you can count on with Yorkie pups is that their colors WILL change. My male is 16 months old and is still pretty much black and tan ... his head is lighter, but he's still pretty dark on his back - but slowly changing. The little girl is 14 months old and is the same way. I actually like the darker colors they are, and hope they don't change too much, but I know they will. That will be OK.
I'm just saying that even though Pup 2 may be darker NOW than Holly was, it doesn't mean that she won't lighten up in color.
Good luck with your decision. Perhaps it will be a Happy New Year after all!