[Hans]

After uploading the .htaccess file, it does not disappear, but it is hidden.

Make sure that the use of .htaccess files is allowed, by adding the following to the Apache directives field within ISPConfig for that site:
<Directory "/var/www/web#/web">
Options FollowSymLinks
AllowOverride All
</Directory>

Note: web# is the webnumber as created by ISPConfig.

Alternative:
Allow the use of .htaccess files on your server globaly, by changing AllowOverride None into AllowOverride All within your Apache configuration file.
Restart Apache afterwards.