Your flex portlets should share the same cookies and authentication for requests as the rest of the portlets. If you were trying to share information between JSP portlets and your Flex portlets, you'd have to have some additional servlets that the Flex would call in order to get that information into the web application sessions, and then there may be other inter portlet communication issues, under JSR-168 portlets we did this with custom http filters that would get the information into the correct sessions. If you've got a JSR-286 (Portal 2.x) container there are other inter portlet communication options, but I don't have any direct experience with them to date, so I can't really advise you on how to do it.
hth