Actually one of the lesser know facts about Toy Story is that Bo actually didn't belong to Andy, that was actually his kid sister Molly's lamp doll, he just liked playing with her as Woody's "damsel in distress." So most people figure Bo belonged to Andy, she didn't, she was Molly's. Which when you think about it, makes even more sense that she's gone, since it was shown at the very start, Molly is not as "sentimental" about her toys as Andy is, since she gave Barbie anyway without even thinking about it and mocks Andy for keeping his some of his older toys. Mrs. Potato Head was originally suppose to be Molly's as well, but for whatever reason, Andy seems to be the owner of her.
And actually if you get to watch Toy Story again, Bo is seen in the flashbacks, look closer at the part where he's watching TV with his toys. She's there. It's easy to miss her, since you're mainly focus on Andy and when Andy gives Rex some popcorn, but she's there.