I do not know if there is a correct way, but we upgraded our "http-passthru.phar" today the following way:
- Disabled the plugin
- Removed the old auth-passthru.phar from /include/plugins
- Copied the new auth-passthru.phar to /include/plugins
- Re-Enabled the auth-passthru plugin
Can't tell you how the storage-fs or ldap auth plugins behave, so I suggest to backup everthing and then just test upgrading the plugins ;)