Ubuntu – How to check the home directory is encrypted in Ubuntu 12.04

My comment above is the correct answer. Apparently writing everything out and then reading over it made something click in my head. Should anyone else find this with a similar problem, check to see what happens when you mount and unmount your private folder with 'ecryptfs-mount-private' and 'ecryptfs-umount-private' respectively. Each should reflect as a change in files displayed in your home directory. As ecryptfs prompts, you need to cd to /home/my_user to see the change reflected.

In my case to "fix" the problem I need to:

• Log in over SSH as normal
• Copy all contents of '~' to another location
• Edit '~/.profile' to add 'ecryptfs-mount-private' at the end (prompts for password to decrypt home after successful SSH login)
• Use 'ecryptfs-mount-private' to mount encrypted home
• Change directory to home, even if it's the current directory (cd /home/my_user)
• Copy files back into home directory
• Profit!

I think you want ecryptfs-recover-private to "recover data from [your] encrypted home or encrypted private partitions. It is useful to run this from a LiveISO or a recovery image." It can use your old login passphrase to unwrap your ecrypfs mount passphrase and access your data.

You could also use ecryptfs-unwrap-passphrase with your old login passphrase to find out what the ecryptfs mount passphrase is directly.