I use this .htaccess to protect my WP installation, but after deactivating "folder protection", the whole .htaccess disappears, not only protection lines.
Yes, thats correct. If you add other lines to the .htaccesss file created by the folder protection feature, they will get removed when you delete the foilder protection. So if you want to use a custom.htaccess file, then its better to add the .htaccess lines for authentification manually.
