Cognos Express has an internal backup tool that collects almost everything into a single backup. It is run from the Cognos Express Manager screen manually. By default it stores the backups it creates inside the installation folders of CX. Saved here, they are easily lost and also easy to delete when upgrading Cognos Express (where you need to do a full uninstall). As you need to restore one of these backups after upgrade this could be problematic, to say the least.
It is easy to change the default Cognos Express backup location. Just go to Cognos Express Manager, click Manager, then Configure and then set backup location to a new location, say c:\cognos_express_backups.
For an in depth discussion of Cognos Express backups, please see our guide to creating an effective Cognos Express backup strategy.