There are several quality solutions for deep linking a flex application or site. For seo purposes which one produces the best indexing results?
Asual's SWFAddress, Adobe's BrowserManager or urlKit. All three of which seem viable and easy to implement.
Update This guy at unitedmindset seems to have pulled it off using the BrowserManager and SWFObject.
The deep-linking libraries would not affect page rank or any SEO result directly. It mostly depends on how you put your alternative content. It is because most search engine do not run JavaScript, which the deep-linking libraries built on, so they wouldn't see the deep-links.
But one thing worth mentioning is, Google can detect and index Flash contents (deep-linked or not), when the swf is embedded by Adobe's solution (AC_OETags.js) or the more standard SWFObject. You may see Google's Webmaster Central Blog.