I'm guessing the reason you are asking for this is because of the bug logged with printing secured featurelayers from a secured custom print task not working correctly? This problem is not specific to Flex. We've done some testing though and have determined that the problem occurs only in 10.1. I don't know if 10.2 is an option for you at this time, if so this would take care of it.
Not sure if this helps you, but wanted to let you know.