After the recompose, user data and config should be preserved IF this is a.) a persistent pool, and b.) The pool is set to redirect data to a seperate disk.
Or if you have roaming profiles set up, in which case persistence and datastores don't come into it.
If you are referring to third party app config data, that might depend on how the app was written. As long as it writes their data to the user's profile, the above stays true.
