This is a manual process, once step. You need to remove the file. Then it can be recreated.
e. g. Valid eCryptfs headers not found in file header region or xattr region, inode 123344
You will need to inode number in bold. Then use this command to find out which file it corresponds to:
find ~/ -inum 123344
I'm assuming here that the ecryptfs is mounted in your home directory, as e.g. in Ubuntu.
Then this gives me some filename, e.g.
To check it's really the problem try to read the file:
You should get an input output error now. If so, feel free to remove the file: