tl;dr; I don’t recommend using Déjà Dup to hold your data when you upgrade distros (e.g. from Ubuntu 11.04 to 11.10) without understanding the risks.
I’m the maintainer of the Déjà Dup backup tool that will be included by default in Ubuntu 11.10. So I’m generally biased in its favor. But I am also a cautious person.
My concern stems from the fact that Déjà Dup uses an opaque backup format . Which means that it does not store your data in plain files that you can just copy back into place with the file manager. You’ll need to use Déjà Dup again to restore them . Which is fine if Déjà Dup is working correctly, as it should.
But just from a risk management perspective, I always recommend that people try to have at least one copy of their data in “plain files” format at all times.
So if you back up with Déjà Dup, then wipe your disk to put Ubuntu 11.10 on there, you’re temporarily going down to zero “plain file” copies of your data. And if anything should go wrong with Déjà Dup, you’ll be very sad.
Here are a few recommended ways to upgrade:
- Use the Ubuntu CD’s built-in upgrade support. It will leave your personal files alone, but upgrade the rest of the system.
- Use the Update Manager to upgrade your machine. Again, this will leave all your personal files in place.
- Copy your files to an external hard drive with your file manager and copy them back after install.
In my mind, a backup system’s primary use case is disaster recovery, where going down to zero “plain file” copies of your data is unintentional and an acceptable risk. Intentionally reducing yourself to zero copies seems unnecessary.
Hopefully, all this caution is overblown. I just want people to be aware of the risks.
 Déjà Dup uses an opaque format to support a feature set that just can’t be done with plain files:
- Incremental backups
- Assuming little about the backup location (allowing cloud backups)
- Supporting file permissions, even when backing up to locations that don’t
 There are technically ways to recover without going through the Déjà Dup interface. They just aren’t very user-friendly.