Because the file FormatAreaStyles.css has moved to a new location, back up your original (located in %TRIDION_HOME%\web\WebUI\Editors\CME\Configuration\ to a safe location.
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Backing up TCM54.config
Modifying your Safeguard configuration
Preparing to upgrade SiteEdit to Experience Manager
Restoring FormatAreaStyles.css
Preparing for the Content Manager server upgrade
Styles configuration