https://askubuntu.com/questions/1092...-so-much-space

/home/.ecryptfs/user is where your encrypted home files are actually kept.
/home/user is just a virtual mountpoint for the decrypted versions of your files; it takes up no real on-disk space.
Deleting files in one place will delete the corresponding files in the other. Since you've likely got filename encryption enabled, it won't be obvious what the files in the .ecryptfs folder are, so only delete files from /home/user .