As you already know, Microsoft updates frequently the DirSync tool used to synchronize your on premises directory with Office 365.
Also, as Microsoft has announced the availability of the S/MIME feature on Exchange 2013 SP1 – and so also for Exchange Online on Office 365, you will have to update your DirSync currently installed.
Download the new version here http://go.microsoft.com/fwlink/?LinkID=278924 – version involved for this post is 1.0.6635.43
Then you have the choice to upgrade the existing installation or uninstalling the installed version one before installing the new one.
NOTE if you uninstall the installed version, you user will continue to be present on Office 365, only updates (new users, details updates) will be synchronize once the new version will be installed.
Then, once the new version has been installed (whatever the process used), open the MIIS client console; run the miisclient.exe file available within C:\Program Files\Windows Azure Active Directory Sync\SYNCBUS\Synchronization Service\UIShell directory.
to confirm/reconfigure your synchronization filtering.
Then check if the userSMIMECertificate attribute is present and enabled; if not present you are not using the correct version of DirSync, if not enabled just enable it.
To check this, go through the MIIS console to the Select Attributes section of the Active Directory management agent (Active Directory Connector)