Rick,
The answer to your question is yes, under almost all circumstances the independent is bailed off. The main reason is not to flatten the wheels on the locomotives or to cause an excessive run-in by the equipment. The preferable way to stop is to apply the automatic (train) brakes and keep the locomotives in power, pulling on the train until the train pulls you to a stop.
After you stop rolling, you can then set your independent.
In this way, the slack is stretched so when the brakes release there is no run-out to knock the passengers off their feet or to damage the lading on your freight train.
Rick Steele