had been changing- this is past perfect continuous. It implies that the change continued for some time in the past before another activity in the past.
had changed- this is the past perfect. It implies that the change happened before something else in the past, there is less focus on the time it took.
Often we add a duration with past perfect continuous or it might be implied in conversation.
The color of the water had been changing for 2 weeks when residents decided to complain.
The color of the water had changed so the residents decided to complain.