The backup file does contains all the data needed to resurrect the entire database, including imported items. There is, however, an advanced setting that one can set so the backup does not included the imported items. By default, Imported Items are INCLUDED in the backups.
The Restore Utility (found in the Amazing Charts directory) is capable of resurrecting the data from the backup (.enc) file.
What happens when you try to backup directly to the flash? What error do you get?