Well I recently saw and read about the Disney's D23 Expo.
It states that Toy Story 4 will be about Woody and Buzz Lightyear going on an adventure trying to find Bo Peep. So what ever did happen to her? The plot in which will be presented to us in the release on June 16th, 2017, will tell us what happened to her.
Although it clearly states that she was sold in the yard sale after Toy Story 2 therefore she only apears as a flashback in Toy Story 3.
Bo Peep indeed is one of the important "Toys" in Woody's life. She is his soul mate. It is obvious that in some way he misses her and wants to find her some way or another. Bo Peep didnt come out in Toy Story 3 at all so Toy Story 4 will give us a new adventure in which all ages will love.
Bo Peep is misunderstood she is not Andy's toy she is Actually Molly's. Bo peep and her sheep belong on Molly's lamp side. It is misunderstood because Andy uses her as the Damsel in Distress that woody saves. She is an important character that is even suitable for Woody. She is always worried for him and always supporting him so in Toy Story 4 there will be a Damsel in Distress waiting for Woody's Rescue