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I installed Ubuntu 12.04 and checkmarked to encrypt my home folder.

How do I backup my home directory at a later time?

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Am I mistaken in believing that deja dup can handle that? – Mahesh Jun 21 '12 at 5:25
Just backup like normal. If you want your backup to also be encrypted, just use that option in Deja-Dup, the backup program. Note that if you just copy your files to a USB drive manually, they won't be encrypted. – Tom Brossman Jun 21 '12 at 5:45
The manual way is to backup /home/.ecryptfs/.Private OR ~/.Private which is a symlink. That data is the encrypted, and /home is what you see while login and auto mounted the cyphered volume/data. Testing is so easy. Copy into an USB then look it into another SO or computer. This is a common mistake :/ i guess. Look into /home/.ecryptfs/user/.ecryptfs OR ~/.ecryptfs to see more info. For better restoring, save that folder too into a safe location. – erm3nda Aug 22 '15 at 15:39

If you are logged in then your homefolder is unencrypted, and you can backup like normal.

The only protection an encrypted home folder provides is when the computer is off and you haven't entered the password yet.

I just rsync my home folder to an offsite location so that it is safe and sound should I ever need to restore it.

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