By doing sudo zebrasrv -D -f /etc/koha/koha-conf.xml I can get search results again:

biblios@debian:~$ sudo zebrasrv -D -f /etc/koha/koha-conf.xml
[sudo] password for biblios:
14:16:39-25/10 [log] zebra_start 2.0.44 419ad759807269fdfa379799a051ed3a551c6541
14:16:39-25/10 [log] config /etc/koha/zebradb/zebra-biblios.cfg
14:16:39-25/10 [log] Loaded filter module /usr/lib/idzebra-2.0/modules/mod-text.so
14:16:39-25/10 [log] Loaded filter module /usr/lib/idzebra-2.0/modules/mod-dom.so
14:16:39-25/10 [log] Loaded filter module /usr/lib/idzebra-2.0/modules/mod-grs-regx.so
14:16:39-25/10 [log] Loaded filter module /usr/lib/idzebra-2.0/modules/mod-grs-marc.so
14:16:39-25/10 [log] Loaded filter module /usr/lib/idzebra-2.0/modules/mod-alvis.so
14:16:39-25/10 [log] Loaded filter module /usr/lib/idzebra-2.0/modules/mod-grs-xml.so
14:16:39-25/10 [log] zebra_start 2.0.44 419ad759807269fdfa379799a051ed3a551c6541
14:16:39-25/10 [log] config /etc/koha/zebradb/zebra-authorities.cfg
14:16:39-25/10 [log] Loaded filter module /usr/lib/idzebra-2.0/modules/mod-text.so
14:16:39-25/10 [log] Loaded filter module /usr/lib/idzebra-2.0/modules/mod-dom.so
14:16:39-25/10 [log] Loaded filter module /usr/lib/idzebra-2.0/modules/mod-grs-regx.so
14:16:39-25/10 [log] Loaded filter module /usr/lib/idzebra-2.0/modules/mod-grs-marc.so
14:16:39-25/10 [log] Loaded filter module /usr/lib/idzebra-2.0/modules/mod-alvis.so
14:16:39-25/10 [log] Loaded filter module /usr/lib/idzebra-2.0/modules/mod-grs-xml.so
14:16:39-25/10 [server] Adding dynamic listener on unix:/var/run/koha/zebradb/bibliosocket id=1
14:16:39-25/10 [server] Adding dynamic listener on unix:/var/run/koha/zebradb/authoritysocket id=2

When starting Debian it mentions in it's startup it's starting koha-zebra-daemon and koha-zebraqueue-daemon.

However, when I do a 'koha-zebra-daemon-start' followed after waiting a bit by 'koha-zebra-daemon-stop' it tells me: daemon: fatal: failed to stop the koha-zebra-ctl.koha daemon: No such process

So I am pretty sure it's not running. Does anybody have any idea what might have gone wrong? The only thing I did was upgrade from 3.00.04 to 3.00.06 and it used to run fine in 3.00.04.

biblios@debian:~$ sudo /etc/init.d/koha-zebra-daemon start
Starting Zebra Server
biblios@debian:~$ sudo /etc/init.d/koha-zebra-daemon stop
Stopping Zebra Server
daemon: fatal: failed to stop the koha-zebra-ctl.koha daemon: No such process
biblios@debian:~$ sudo /etc/init.d/koha-zebraqueue-daemon start

Starting Zebraqueue Daemon
biblios@debian:~$ sudo /etc/init.d/koha-zebraqueue-daemon stop
Stopping Zebraqueue Daemon
daemon: fatal: failed to stop the koha-zebraqueue-ctl-koha daemon: No such process