Relevant output from /usr/bin/zkt-signer -v -v:
[some zones signed just fine or did not need to resign... those have been removed]

parsing zone "dmz.freshdot.net." in dir "/etc/bind/master/net/freshdot.net/dmz.freshdot.net"
        Check RFC5011 status
                ->not a rfc5011 zone, looking for a regular ksk rollover
        Check KSK status
        Check ZSK status
        Re-signing necessary: re-signing interval (2w) reached
        Writing key file "/etc/bind/master/net/freshdot.net/dmz.freshdot.net/dnskey.db"
        Incrementing serial number in file "/etc/bind/master/net/freshdot.net/dmz.freshdot.net/zone.db"
        Signing zone "dmz.freshdot.net."
could not increment serialno of domain vm.freshdot.net. in file /etc/bind/master/net/freshdot.net/vm.freshdot.net/zone.db: no serial number found in zone file!
could not increment serialno of domain freshdot.net. in file /etc/bind/master/net/freshdot.net/zone.db: no serial number found in zone file!
could not increment serialno of domain thesmallprint.nl. in file /etc/bind/master/nl/thesmallprint.nl/zone.db: no serial number found in zone file!
          Run cmd "cd /etc/bind/master/net/freshdot.net/dmz.freshdot.net; /usr/sbin/dnssec-signzone  -u -3 AFB31E -C -g -o dmz.freshdot.net. -e +1814400  zone.db K*.private 2>&1"
          Cmd dnssec-signzone return: "zone.db.signed"
        Signing completed after 0s.
          copy "/etc/bind/master/net/freshdot.net/dmz.freshdot.net/keyset-dmz.freshdot.net." to parent dir

parsing zone "vm.freshdot.net." in dir "/etc/bind/master/net/freshdot.net/vm.freshdot.net"
        Check RFC5011 status
                ->not a rfc5011 zone, looking for a regular ksk rollover
        Check KSK status
        Check ZSK status
        Re-signing necessary: re-signing interval (2w) reached
        Writing key file "/etc/bind/master/net/freshdot.net/vm.freshdot.net/dnskey.db"

parsing zone "freshdot.net." in dir "/etc/bind/master/net/freshdot.net"
        Check RFC5011 status
                ->not a rfc5011 zone, looking for a regular ksk rollover
        Check KSK status
        Check ZSK status
        Re-signing necessary: Modified KSK in delegated domain
        Writing key file "/etc/bind/master/net/freshdot.net/dnskey.db"
          copy "/etc/bind/master/net/freshdot.net/keyset-freshdot.net." to parent dir

parsing zone "thesmallprint.nl." in dir "/etc/bind/master/nl/thesmallprint.nl"
        Check RFC5011 status
                ->not a rfc5011 zone, looking for a regular ksk rollover
        Check KSK status
        Check ZSK status
        Re-signing necessary: re-signing interval (2w) reached
        Writing key file "/etc/bind/master/nl/thesmallprint.nl/dnskey.db"
          copy "/etc/bind/master/nl/thesmallprint.nl/keyset-thesmallprint.nl." to parent dir

parsing zone "degast.org." in dir "/etc/bind/master/org/degast.org"
        Check RFC5011 status
                ->not a rfc5011 zone, looking for a regular ksk rollover
        Check KSK status
        Check ZSK status
        Re-signing not necessary!
        Check if there is a parent file to copy
          copy "/could not increment serialno of domain freshdot.org. in file /etc/bind/master/org/freshdot.org/zone.db: no serial number found in zone file!
etc/bind/master/org/degast.org/keyset-degast.org." to parent dir

parsing zone "freshdot.org." in dir "/etc/bind/master/org/freshdot.org"
        Check RFC5011 status
                ->not a rfc5011 zone, looking for a regular ksk rollover
        Check KSK status
        Check ZSK status
        Re-signing necessary: re-signing interval (2w) reached
        Writing key file "/etc/bind/master/org/freshdot.org/dnskey.db"
          copy "/etc/bind/master/org/freshdot.org/keyset-freshdot.org." to parent dir