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How can I change the UID of a user with an encrypted home directory?

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You first need to logout the user you want to modify and kill all processes he runs.
A good approach is to restart and log in as root or as another sudo user.

To enable the root user execute the following commands.

$ sudo su
# passwd

Now you can log in using root and the password you provided. Once logged in as root execute

# usermod -u newUID myuser

to change myuser's uid and

# chown -R myuser /home/.ecryptfs/myuser

to change the owner of the encrypted files.
You should now be able to log out and log back in as myuser.

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