Yes, Maya's relationship with Bailey changes through the course of the book. The easiest reason for this is that they grow up and need one another less. Look at the way they depend on one another intensely early in the book and compare that to the intelligent independence manifest in the final pages and you'll see what I mean.
More specifically, their relationship changes when they encounter outside forces that have different impacts on them. For example, Mr. Freeman's abuse/rape of Maya draws her close to Bailey, but it also changes their relationship. She's fractured and turned inward by the pain, while Bailey is not. The appearance of their parents at various times also tugs them in different directions; the different relationships they have with their parents change their relationships.