Facebook apps probably store their data online, using Facebook APIs, not on the local computer otherwise you'd lose all your game data if you signed in using another computer.

Flash shared objects are store in the Application Data folder, which is under C:\Documents and Settings\USERNAME\Application Data so they are not in a temporary location. Any "cleaner" app that removes another applications data from the Application Data folder is broken.

If you're doing this online you can't control where the SO is created (well you can, but you can't change it very much) so you should store your data online where it's safe.

If you're doing this offline, in a projector, then you'll probably have to spring for a third party SWF2EXE tool to let you control where your data gets saved or wanr your users not to run "cleaner" tools or they risk losing their data.