Has anybody seen any really great examples of how a company handles change management? Or any advice on how to manage change management for B2B customers in a fast-paced agile startup?

This is a pretty complex question. Internal change management is different from external towards customers. While there is influence from external factors - because of trends in your particular segment, competitive pressures, new technologies that disrupt your existence and so on. How you serve your existing customers as you transition to new innovation, new product introductions etc is very important. It all depends on how much of your revenue is impacted by the transition. 

Without knowing a specific scenario -- this is hard one to answer. 

I recommend reading Lou Gerstner's "Elephants Can dance" book about how he turned around IBM. Great read.