Hi
this question was asked 2 years back - I would like to follow up if anything has changed or will change so as an app developer you are able to control which instance will shutdown in case the instance count was changed - here a few old threads that discuss this and come to the conclusion it is currently not controllable by the developer and that in most cases the instance with the highest instance index count is selected by the fabric controller (but this is not guaranteed).
Thanks!
http://stackoverflow.com/questions/9030706/which-instances-are-stopped-when-i-scale-my-azure-role-down