Manually backup and restore all partitions
The reason for warning regarding backup is, that dd just copies block wise everything, not caring about content. It clones the partition. Of course you can use dd also for backup the /system or /data partitions in recovery mode.
But in normal mode you should not use dd for mounted partitions, because content may change during progress (Android is running) and you probably get inconsistent/unreadable result. Unmount the partition first.
Another way is to create a tarball archive. That is what nandroid backup does. But with the same warning - better to do this &quot;offline&quot; in recovery mode, and not in normal mode.