Hi,
 See the relevant parts of the config and also the log below. There
 were no updates to the zone, I have flushed journal to file, performed
 zone-status command followed by knotc reload. Then I can see that zone
 is re-signed an zone transfer follows (KNOT is a hidden master),
 Configuration (just rozjezdy.cz choosen as an example):
 policy:
   - id: tmcz-default
     algorithm: ecdsap256sha256
     zsk-lifetime: 30d
     ksk-lifetime: 90d
     nsec3: on
     nsec3-salt-length: 16
     cds-cdnskey-publish: always
     propagation-delay: 1d
     ksk-submission: nic.cz
 template:
   - id: signed
     storage: "/var/lib/knot/signed"
     file: "db.%s"
     serial-policy: unixtime
     disable-any: on
     semantic-checks: on
     module: mod-rrl/rrl-10
     module: mod-stats/custom
     notify: idunn-freya
     acl: [allowed_transfer]
     dnssec-policy: tmcz-default
     dnssec-signing: on
 zone:
   - domain: rozjezdy.cz
     template: signed
 root@idunn:/etc/knot# knotc  zone-status rozjezdy.cz
 [rozjezdy.cz.] role: master | serial: 1513089643 | transaction: none |
 freeze: no | refresh: not scheduled | update: not scheduled |
 expiration: not scheduled | journal flush: not scheduled | notify: not
 scheduled | DNSSEC re-sign: +6D17h31m18s | NSEC3 resalt: +22D22h35m50s
 | parent DS query: not scheduled
 root@idunn:/etc/knot#
 root@idunn:~# journalctl -u knot -f  | grep rozjezdy
 Dec 12 17:03:34 idunn knotd[4604]: info: [rozjezdy.cz.] control,
 received command 'zone-status'
 Dec 12 17:06:42 idunn knotd[4604]: info: [rozjezdy.cz.] control,
 received command 'zone-flush' 
I don't understand the following re-sign. Was it triggered by a zone
change?
  Dec 12 17:07:11 idunn knotd[4604]: info:
[rozjezdy.cz.] DNSSEC, signing
 zone
 Dec 12 17:07:11 idunn knotd[4604]: info: [rozjezdy.cz.] DNSSEC, key,
 tag 52375, algorithm ECDSAP256SHA256, KSK, public, active
 Dec 12 17:07:11 idunn knotd[4604]: info: [rozjezdy.cz.] DNSSEC, key,
 tag 53957, algorithm ECDSAP256SHA256, public, active
 Dec 12 17:07:11 idunn knotd[4604]: info: [rozjezdy.cz.] DNSSEC, signing
 started
 Dec 12 17:07:11 idunn knotd[4604]: info: [rozjezdy.cz.] DNSSEC,
 successfully signed
 Dec 12 17:07:11 idunn knotd[4604]: info: [rozjezdy.cz.] DNSSEC, next
 signing at 2017-12-19T10:34:52
 Dec 12 17:07:11 idunn knotd[4604]: info: [rozjezdy.cz.] zone file
 updated, serial 1513089643 -> 1513094831
 Dec 12 17:07:12 idunn knotd[4604]: info: [rozjezdy.cz.] notify,
 outgoing, 93.153.117.50@53: serial 1513094831
 Dec 12 17:07:13 idunn knotd[4604]: info: [rozjezdy.cz.] IXFR,
 outgoing, 93.153.117.50@40241: started, serial 1513089643 ->
 1513094831
 Dec 12 17:07:13 idunn knotd[4604]: info: [rozjezdy.cz.] IXFR,
 outgoing, 93.153.117.50@40241: finished, 0.00 seconds, 1 messages, 705
 bytes
 Dec 12 17:07:14 idunn knotd[4604]: info: [rozjezdy.cz.] IXFR,
 outgoing, 93.153.117.20@40111: started, serial 1513089643 ->
 1513094831
 Dec 12 17:07:14 idunn knotd[4604]: info: [rozjezdy.cz.] IXFR,
 outgoing, 93.153.117.20@40111: finished, 0.00 seconds, 1 messages, 705
 bytes
 root@idunn:/etc/knot# knotc  zone-status rozjezdy.cz
 [rozjezdy.cz.] role: master | serial: 1513094831 | transaction: none |
 freeze: no | refresh: not scheduled | update: not scheduled |
 expiration: not scheduled | journal flush: not scheduled | notify: not
 scheduled | DNSSEC re-sign: +6D17h27m3s | NSEC3 resalt: +22D22h31m35s
 | parent DS query: not scheduled
 root@idunn:/etc/knot#
 I have not checked it in a detail nevertheless is seems that all zones
 are re-signed:
 Dec 12 17:03:34 idunn knotd[4604]: info: [rozjezdy.cz.] control,
 received command 'zone-status'
 Dec 12 17:06:42 idunn knotd[4604]: info: [rozjezdy.cz.] control,
 received command 'zone-flush'
 Dec 12 17:07:01 idunn knotd[4604]: info: control, received command
 'reload'
 Dec 12 17:07:01 idunn knotd[4604]: info: reloading configuration file
 '/etc/knot/knot.conf'
 Dec 12 17:07:08 idunn knotd[4604]: info: configuration reloaded
 Dec 12 17:07:08 idunn knotd[4604]: info: [
test.net.] DNSSEC, signing
 zone
 Dec 12 17:07:08 idunn knotd[4604]: info: [5gnet.cz.] DNSSEC, signing
 zone
 Dec 12 17:07:09 idunn knotd[4604]: info: [
test.net.] DNSSEC, key, tag
 31290, algorithm ECDSAP256SHA256, KSK, public, ready, active
 Dec 12 17:07:09 idunn knotd[4604]: info: [5gnet.cz.] DNSSEC, key, tag
 50849, algorithm ECDSAP256SHA256, KSK, public, active
 Dec 12 17:07:09 idunn knotd[4604]: info: [
test.net.] DNSSEC, key, tag
 51884, algorithm ECDSAP256SHA256, public, active
 Dec 12 17:07:09 idunn knotd[4604]: info: [5gnet.cz.] DNSSEC, key, tag
 40637, algorithm ECDSAP256SHA256, public, active
 Dec 12 17:07:10 idunn knotd[4604]: info: [
test.net.] DNSSEC, signing
 started
 Dec 12 17:07:10 idunn knotd[4604]: info: [
test.net.] DNSSEC, zone is
 up-to-date
 Dec 12 17:07:10 idunn knotd[4604]: info: [
test.net.] DNSSEC, next
 signing at 2017-12-14T13:22:15
 Dec 12 17:07:10 idunn knotd[4604]: info: [mych5.cz.] DNSSEC, signing
 zone
 Dec 12 17:07:10 idunn knotd[4604]: info: [mych5.cz.] DNSSEC, key, tag
 53237, algorithm ECDSAP256SHA256, KSK, public, active
 Dec 12 17:07:10 idunn knotd[4604]: info: [mych5.cz.] DNSSEC, key, tag
 36052, algorithm ECDSAP256SHA256, public, active
 Dec 12 17:07:10 idunn knotd[4604]: info: [5gnet.cz.] DNSSEC, signing
 started
 Dec 12 17:07:10 idunn knotd[4604]: info: [5gnet.cz.] DNSSEC, zone is
 up-to-date
 Dec 12 17:07:10 idunn knotd[4604]: info: [5gnet.cz.] DNSSEC, next
 signing at 2017-12-15T14:01:52
 Dec 12 17:07:10 idunn knotd[4604]: info: [t-run.cz.] DNSSEC, signing
 zone
 Dec 12 17:07:10 idunn knotd[4604]: info: [t-run.cz.] DNSSEC, key, tag
 11563, algorithm ECDSAP256SHA256, KSK, public, active
 Dec 12 17:07:10 idunn knotd[4604]: info: [t-run.cz.] DNSSEC, key, tag
 39847, algorithm ECDSAP256SHA256, public, active
 Dec 12 17:07:10 idunn knotd[4604]: info: [mych5.cz.] DNSSEC, signing
 started
 Dec 12 17:07:10 idunn knotd[4604]: info: [mych5.cz.] DNSSEC, zone is
 up-to-date
 Dec 12 17:07:10 idunn knotd[4604]: info: [mych5.cz.] DNSSEC, next
 signing at 2017-12-15T08:26:15
 Dec 12 17:07:10 idunn knotd[4604]: info: [tnews.cz.] DNSSEC, signing
 zone
 Dec 12 17:07:10 idunn knotd[4604]: info: [tnews.cz.] DNSSEC, key, tag
 30976, algorithm ECDSAP256SHA256, KSK, public, ready, active
 Dec 12 17:07:10 idunn knotd[4604]: info: [tnews.cz.] DNSSEC, key, tag
 26699, algorithm ECDSAP256SHA256, public, active
 Dec 12 17:07:11 idunn knotd[4604]: info: [t-run.cz.] DNSSEC, signing
 started
 Dec 12 17:07:11 idunn knotd[4604]: info: [tnews.cz.] DNSSEC, signing
 started
 Dec 12 17:07:11 idunn knotd[4604]: info: [t-run.cz.] DNSSEC,
 successfully signed
 Dec 12 17:07:11 idunn knotd[4604]: info: [tnews.cz.] DNSSEC, zone is
 up-to-date
 Dec 12 17:07:11 idunn knotd[4604]: info: [tnews.cz.] DNSSEC, next
 signing at 2017-12-19T16:39:13
 Dec 12 17:07:11 idunn knotd[4604]: info: [t-news.cz.] DNSSEC, signing
 zone
 Dec 12 17:07:11 idunn knotd[4604]: info: [t-news.cz.] DNSSEC, key, tag
 26662, algorithm ECDSAP256SHA256, KSK, public, ready, active
 Dec 12 17:07:11 idunn knotd[4604]: info: [t-news.cz.] DNSSEC, key, tag
 38793, algorithm ECDSAP256SHA256, public, active
 Dec 12 17:07:11 idunn knotd[4604]: info: [t-news.cz.] DNSSEC, signing
 started
 Dec 12 17:07:11 idunn knotd[4604]: info: [t-news.cz.] DNSSEC, zone is
 up-to-date
 Dec 12 17:07:11 idunn knotd[4604]: info: [t-news.cz.] DNSSEC, next
 signing at 2017-12-19T16:39:13
 Dec 12 17:07:11 idunn knotd[4604]: info: [tcrowd.cz.] DNSSEC, signing
 zone
 Dec 12 17:07:11 idunn knotd[4604]: info: [tcrowd.cz.] DNSSEC, key, tag
  1752, algorithm ECDSAP256SHA256, KSK, public, ready, active
 Dec 12 17:07:11 idunn knotd[4604]: info: [tcrowd.cz.] DNSSEC, key, tag
 30878, algorithm ECDSAP256SHA256, public, active
 Dec 12 17:07:11 idunn knotd[4604]: info: [t-run.cz.] DNSSEC, next
 signing at 2017-12-13T09:52:40
 Dec 12 17:07:11 idunn knotd[4604]: info: [tmusic.cz.] DNSSEC, signing
 zone
  
Ok, during the server reload all zones are checked for re-sign
necessity:
Dec 12 17:07:10 idunn knotd[4604]: info: [
.] DNSSEC, signing
started
If the zone wasn't re-signed, this message is logged:
Dec 12 17:07:10 idunn knotd[4604]: info: [
.] DNSSEC, zone is
up-to-date
Of course, in the case of many zones the full reload takes some time.
How
many zones do you have configured?
You should increase the control timeout on the server side: