If it's a non-boot drive, format the destination encrypted and use Smart Update.
If it's a boot drive, start up from the backup. Use Recovery Partition Creator (
http://musings.silvertooth.us) or reinstall the OS from the App Store to create a recovery volume. Then, turn on encryption in System Preferences.
Once done, you don't have to wait for it to finish. Boot back to the regular volume. Future updates should be made with Smart Update, and encryption and bootability should be maintained.