It all depends on how many custom images and how much custom code you've used in your site. In Flex 2, you used to upload the images to the theme's images folder and link to them using just the image name. But with Flex 3, you upload images into the WP media library and link to them using the full URL. So those would need to change.
If you've customized the feature.php or footer.php files, you would need to manually transfer any changes into Flex 3.