Why don’t you write a quick plugin … called “is user logged in” that registers a URL call.
So the user hits the page, then the Flash or Java could just hit:
http://mysite.com/customurl?hash=wordpress_logged_in_[hash]
Then the plugin would run and return true or false.
References:
http://codex.wordpress.org/WordPress_Cookies#WP_.3E_3
This way you keep everything within reach of the WordPress core toolset. So if you need to access the authentication API or any other tools you can.
If you do end up going this route I recommend making use of the Rewrite API:
http://codex.wordpress.org/WordPress_API's
Best of luck!
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