Solved
Somehow the website was assigned the wrong values in the title, doctype_id and doctype_id in the isp_nodes table of the ispconfigdb. I restored the old values and restarted apache and ispconfig. The website is showing again in the config panel.
host:~# mysql -u root -p
mysql> use ispconfigdb;
mysql> select * from isp_nodes;
mysql> update isp_nodes set title = 'domain.tld' where tree_id = 7;
mysql> update isp_nodes set doctype_id = '1013' where tree_id = 7;
mysql> update isp_nodes set parent = '3' where tree_id = 7;
mysql> \q
host:~# /etc/init.d/ispconfig_server restart
host:~# /etc/init.d/apache2 restart
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