Ssh – Changing copssh default FTP root breaks RSA authentication

To change the passphrase on your default key:

$ ssh-keygen -p

If you need to specify a key, pass the -f option:

$ ssh-keygen -p -f ~/.ssh/id_dsa

then provide your old and new passphrase (twice) at the prompts. (Use ~/.ssh/id_rsa if you have an RSA key.)

More details from man ssh-keygen:

[...]
SYNOPSIS
    ssh-keygen [-q] [-b bits] -t type [-N new_passphrase] [-C comment]
               [-f output_keyfile]
    ssh-keygen -p [-P old_passphrase] [-N new_passphrase] [-f keyfile]
[...]
     -f filename
             Specifies the filename of the key file.
[...]
     -N new_passphrase
             Provides the new passphrase.

     -P passphrase
             Provides the (old) passphrase.

     -p      Requests changing the passphrase of a private key file instead of
             creating a new private key.  The program will prompt for the file
             containing the private key, for the old passphrase, and twice for
             the new passphrase.
[...]

Your first trace looks somewhat strange. As jneves points out ssh assumes that the file contains your public and private keys. The documentation says that the "identity" is the private key.

 -i identity_file
         Selects a file from which the identity (private key) for RSA or DSA authentication is
         read.

If you do indeed have two keys in one file (had no idea it is possible) you should probably separate them. In any case it seems like you are not conforming to the documentation.