I believe they wait until you have successfully completed the assessment before contacting any references. ( I had a pass letter 7 weeks ago and I dont think they have contacted any of mine--course that could be a bad sign!)
In general I would always try to contact my references to give them a heads up and ask their permission to use them as a reference.
In the case of managers and chief pilot one would hope that these people would merely be professionals and therefore should not really require any advance notice.....you may be better off to list them and just wait?