(re)boot issues, how to debug

Since a long time I have issues with booting HAOS. My HAOS is running in a virtual machine on a Synology NAS. Every time HAOS is updated or the Synology needs to reboot (with clean shutdown of the virtual machine), after booting of the virtual machine I always have issue with HA not starting and in the console I can see:

Waiting for the Home Assistant CLI to be ready…
[WARN] Home Assistant CLI not starting! Jumping into emergency console…

I have ssh setup, so I can use the ha commands in ssh (after some time).
Here are the logs from the supervisor:

[core-ssh log]$ ha su logs
2025-04-01 10:58:29.129 INFO (MainThread) [supervisor.docker.interface] Attaching to ghcr.io/home-assistant/amd64-hassio-dns with version 2025.02.0
2025-04-01 10:58:31.431 INFO (MainThread) [supervisor.plugins.dns] Starting CoreDNS plugin
2025-04-01 10:58:49.511 INFO (MainThread) [supervisor.docker.dns] Starting DNS ghcr.io/home-assistant/amd64-hassio-dns with version 2025.02.0 - 172.30.32.3
2025-04-01 10:58:49.512 INFO (MainThread) [supervisor.plugins.dns] Updated /etc/resolv.conf
2025-04-01 10:58:51.331 INFO (MainThread) [supervisor.docker.interface] Attaching to ghcr.io/home-assistant/amd64-hassio-audio with version 2025.02.0
2025-04-01 10:58:53.000 INFO (MainThread) [supervisor.plugins.audio] Starting Audio plugin
2025-04-01 10:59:18.809 INFO (MainThread) [supervisor.docker.audio] Starting Audio ghcr.io/home-assistant/amd64-hassio-audio with version 2025.02.0 - 172.30.32.4
2025-04-01 10:59:18.815 INFO (MainThread) [supervisor.docker.interface] Attaching to ghcr.io/home-assistant/amd64-hassio-observer with version 2025.02.0
2025-04-01 10:59:21.251 INFO (MainThread) [supervisor.docker.interface] Attaching to ghcr.io/home-assistant/amd64-hassio-multicast with version 2025.02.0
2025-04-01 10:59:24.134 INFO (MainThread) [supervisor.plugins.multicast] Starting Multicast plugin
2025-04-01 10:59:40.626 INFO (MainThread) [supervisor.docker.multicast] Starting Multicast ghcr.io/home-assistant/amd64-hassio-multicast with version 2025.02.0 - Host
2025-04-01 10:59:41.521 INFO (MainThread) [supervisor.homeassistant.secrets] Loaded 6 Home Assistant secrets
2025-04-01 10:59:46.991 INFO (MainThread) [supervisor.docker.interface] Attaching to ghcr.io/home-assistant/qemux86-64-homeassistant with version 2025.3.3
2025-04-01 10:59:51.630 INFO (MainThread) [supervisor.os.manager] Detect Home Assistant Operating System 15.1 / BootSlot B
2025-04-01 10:59:51.676 INFO (MainThread) [supervisor.store.git] Loading add-on /data/addons/core repository
2025-04-01 10:59:51.681 INFO (MainThread) [supervisor.store.git] Loading add-on /data/addons/git/45df7312 repository
2025-04-01 10:59:51.729 INFO (MainThread) [supervisor.store.git] Loading add-on /data/addons/git/5c53de3b repository
2025-04-01 10:59:51.746 INFO (MainThread) [supervisor.store.git] Loading add-on /data/addons/git/a0d7b954 repository
2025-04-01 10:59:51.754 INFO (MainThread) [supervisor.store.git] Loading add-on /data/addons/git/d5369777 repository
2025-04-01 10:59:51.782 INFO (MainThread) [supervisor.store.git] Loading add-on /data/addons/git/1904bdd2 repository
2025-04-01 11:00:54.710 INFO (MainThread) [supervisor.store] Loading add-ons from store: 86 all - 86 new - 0 remove
2025-04-01 11:00:55.332 INFO (MainThread) [supervisor.addons.manager] Found 10 installed add-ons
2025-04-01 11:00:56.337 INFO (MainThread) [supervisor.docker.interface] Attaching to homeassistant/amd64-addon-ssh with version 9.16.0
2025-04-01 11:00:56.971 INFO (MainThread) [supervisor.docker.interface] Attaching to ghcr.io/esphome/esphome-hassio with version 2025.3.2
2025-04-01 11:00:57.044 INFO (MainThread) [supervisor.docker.interface] Attaching to homeassistant/amd64-addon-duckdns with version 1.18.0
2025-04-01 11:00:57.296 INFO (MainThread) [supervisor.docker.interface] Attaching to homeassistant/amd64-addon-mosquitto with version 6.5.0
2025-04-01 11:00:57.388 INFO (MainThread) [supervisor.docker.interface] Attaching to homeassistant/amd64-addon-samba with version 12.5.0
2025-04-01 11:00:57.461 INFO (MainThread) [supervisor.docker.interface] Attaching to ghcr.io/sle118/amd64-addon-network-manager-fix with version 1.1.0
2025-04-01 11:00:57.626 INFO (MainThread) [supervisor.docker.interface] Attaching to ghcr.io/hassio-addons/vscode/amd64 with version 5.18.4
2025-04-01 11:00:57.773 INFO (MainThread) [supervisor.docker.interface] Attaching to zigbee2mqtt/zigbee2mqtt-amd64 with version 2.1.3-1
2025-04-01 11:00:58.748 INFO (MainThread) [supervisor.docker.interface] Attaching to homeassistant/amd64-addon-nginx_proxy with version 3.11.1
2025-04-01 11:00:59.070 INFO (MainThread) [supervisor.docker.interface] Attaching to homeassistant/amd64-addon-silabs-flasher with version 0.3.2
2025-04-01 11:01:03.562 INFO (MainThread) [supervisor.backups.manager] Found 14 backup files
2025-04-01 11:01:05.094 ERROR (MainThread) [supervisor.backups.backup] Can't read backup tarfile /data/mounts/NAS1_Backup/3a1d8044.tar: "filename './backup.json' not found"
2025-04-01 11:01:06.254 INFO (MainThread) [supervisor.discovery] Loaded 2 messages
2025-04-01 11:01:06.255 INFO (MainThread) [supervisor.ingress] Loaded 8 ingress sessions
2025-04-01 11:01:06.255 INFO (MainThread) [supervisor.resolution.check] Starting system checks with state setup
2025-04-01 11:01:06.255 INFO (MainThread) [supervisor.resolution.checks.base] Run check for detached_addon_removed/addon
2025-04-01 11:01:06.255 INFO (MainThread) [supervisor.resolution.checks.base] Run check for disabled_data_disk/system
2025-04-01 11:01:06.256 INFO (MainThread) [supervisor.resolution.checks.base] Run check for multiple_data_disks/system
2025-04-01 11:01:06.256 INFO (MainThread) [supervisor.resolution.checks.base] Run check for detached_addon_missing/addon
2025-04-01 11:01:06.256 INFO (MainThread) [supervisor.resolution.check] System checks complete
2025-04-01 11:01:06.256 INFO (MainThread) [supervisor.resolution.evaluate] Starting system evaluation with state setup
2025-04-01 11:01:06.256 INFO (MainThread) [supervisor.resolution.evaluate] System evaluation complete
2025-04-01 11:01:06.257 INFO (MainThread) [supervisor.jobs] 'ResolutionFixup.run_autofix' blocked from execution, system is not running - setup
2025-04-01 11:01:06.259 INFO (MainThread) [supervisor.resolution.evaluate] Starting system evaluation with state setup
2025-04-01 11:01:06.260 INFO (MainThread) [supervisor.resolution.evaluate] System evaluation complete
2025-04-01 11:01:06.264 INFO (MainThread) [__main__] Running Supervisor
2025-04-01 11:01:07.998 INFO (MainThread) [supervisor.os.manager] Rauc: slot B - activated slot kernel.1, marked slot kernel.1 as good
2025-04-01 11:01:08.017 INFO (MainThread) [supervisor.addons.manager] Phase 'initialize' starting 0 add-ons
2025-04-01 11:01:08.961 INFO (MainThread) [supervisor.addons.manager] Phase 'system' starting 1 add-ons
2025-04-01 11:01:27.633 INFO (MainThread) [supervisor.docker.addon] Starting Docker add-on homeassistant/amd64-addon-mosquitto with version 6.5.0
2025-04-01 11:01:32.646 INFO (MainThread) [supervisor.addons.manager] Phase 'services' starting 5 add-ons
2025-04-01 11:01:55.275 INFO (MainThread) [supervisor.docker.addon] Starting Docker add-on ghcr.io/esphome/esphome-hassio with version 2025.3.2
2025-04-01 11:02:23.440 INFO (MainThread) [supervisor.docker.addon] Starting Docker add-on homeassistant/amd64-addon-duckdns with version 1.18.0
2025-04-01 11:02:58.610 INFO (MainThread) [supervisor.docker.addon] Starting Docker add-on homeassistant/amd64-addon-samba with version 12.5.0
2025-04-01 11:03:07.377 INFO (MainThread) [supervisor.services.modules.mqtt] Set core_mosquitto as service provider for mqtt
2025-04-01 11:03:37.633 INFO (MainThread) [supervisor.docker.addon] Starting Docker add-on homeassistant/amd64-addon-ssh with version 9.16.0
2025-04-01 11:03:58.487 INFO (MainThread) [supervisor.api.middleware.security] /network/info access from core_samba
2025-04-01 11:04:10.210 INFO (MainThread) [supervisor.docker.addon] Starting Docker add-on ghcr.io/hassio-addons/vscode/amd64 with version 5.18.4
2025-04-01 11:04:58.617 WARNING (MainThread) [supervisor.addons.addon] Timeout while waiting for addon Samba share to start, took more than 120 seconds
2025-04-01 11:05:30.892 INFO (MainThread) [supervisor.api.middleware.security] /network/info access from core_ssh
2025-04-01 11:05:31.373 INFO (MainThread) [supervisor.api.middleware.security] /network/info access from core_ssh
2025-04-01 11:05:31.376 INFO (MainThread) [supervisor.api.middleware.security] /host/info access from core_ssh
2025-04-01 11:05:31.381 INFO (MainThread) [supervisor.api.middleware.security] /core/info access from core_ssh
2025-04-01 11:05:35.733 WARNING (MainThread) [supervisor.addons.addon] Watchdog found addon Samba share is unhealthy, restarting...
2025-04-01 11:05:35.739 INFO (SyncWorker_2) [supervisor.docker.manager] Stopping addon_core_samba application
2025-04-01 11:05:53.126 INFO (SyncWorker_2) [supervisor.docker.manager] Cleaning addon_core_samba application
2025-04-01 11:06:04.335 INFO (MainThread) [supervisor.resolution.module] Create new suggestion execute_start - addon / core_samba
2025-04-01 11:06:04.339 INFO (MainThread) [supervisor.resolution.module] Create new suggestion disable_boot - addon / core_samba
2025-04-01 11:06:04.339 INFO (MainThread) [supervisor.resolution.module] Create new issue boot_fail - addon / core_samba
2025-04-01 11:06:04.347 WARNING (MainThread) [supervisor.addons.addon] Watchdog found addon Studio Code Server is unhealthy, restarting...
2025-04-01 11:06:04.350 INFO (MainThread) [supervisor.core] Start Home Assistant Core
2025-04-01 11:06:04.359 INFO (SyncWorker_1) [supervisor.docker.manager] Stopping addon_a0d7b954_vscode application
2025-04-01 11:06:04.377 INFO (SyncWorker_5) [supervisor.docker.manager] Starting homeassistant
2025-04-01 11:06:11.767 INFO (MainThread) [supervisor.docker.addon] Starting Docker add-on homeassistant/amd64-addon-samba with version 12.5.0
2025-04-01 11:06:22.636 INFO (SyncWorker_1) [supervisor.docker.manager] Cleaning addon_a0d7b954_vscode application
2025-04-01 11:06:26.215 INFO (MainThread) [supervisor.api.middleware.security] /network/info access from core_samba
2025-04-01 11:06:32.620 INFO (MainThread) [supervisor.homeassistant.core] Wait until Home Assistant is ready
2025-04-01 11:07:04.156 INFO (MainThread) [supervisor.docker.addon] Starting Docker add-on ghcr.io/hassio-addons/vscode/amd64 with version 5.18.4
2025-04-01 11:08:11.777 WARNING (MainThread) [supervisor.addons.addon] Timeout while waiting for addon Samba share to start, took more than 120 seconds
2025-04-01 11:08:14.953 WARNING (MainThread) [supervisor.addons.addon] Watchdog found addon Samba share is unhealthy, restarting...
2025-04-01 11:08:14.965 INFO (SyncWorker_1) [supervisor.docker.manager] Stopping addon_core_samba application
2025-04-01 11:08:24.497 INFO (SyncWorker_1) [supervisor.docker.manager] Cleaning addon_core_samba application
2025-04-01 11:08:49.100 INFO (MainThread) [supervisor.docker.addon] Starting Docker add-on homeassistant/amd64-addon-samba with version 12.5.0
2025-04-01 11:08:58.407 INFO (MainThread) [supervisor.api.middleware.security] /network/info access from core_samba
2025-04-01 11:09:32.966 ERROR (MainThread) [supervisor.homeassistant.core] No Home Assistant Core response, assuming a fatal startup error
2025-04-01 11:09:32.967 ERROR (MainThread) [supervisor.core] Can't start Home Assistant Core - rebuiling
2025-04-01 11:09:33.090 INFO (SyncWorker_1) [supervisor.docker.manager] Stopping homeassistant application
2025-04-01 11:09:42.650 INFO (SyncWorker_1) [supervisor.docker.manager] Cleaning homeassistant application
2025-04-01 11:09:47.737 INFO (MainThread) [supervisor.homeassistant.module] Update pulse/client.config: /data/tmp/homeassistant_pulse
2025-04-01 11:10:12.344 INFO (MainThread) [supervisor.docker.homeassistant] Starting Home Assistant ghcr.io/home-assistant/qemux86-64-homeassistant with version 2025.3.3
2025-04-01 11:10:12.345 INFO (MainThread) [supervisor.homeassistant.core] Wait until Home Assistant is ready
2025-04-01 11:10:49.109 WARNING (MainThread) [supervisor.addons.addon] Timeout while waiting for addon Samba share to start, took more than 120 seconds
2025-04-01 11:12:17.612 INFO (MainThread) [supervisor.homeassistant.api] Updated Home Assistant API token
2025-04-01 11:12:17.615 INFO (MainThread) [supervisor.homeassistant.core] Home Assistant Core state changed to APIState(core_state='NOT_RUNNING', offline_db_migration=False)
2025-04-01 11:12:17.661 INFO (MainThread) [supervisor.api.middleware.security] /supervisor/logs access from core_ssh
2025-04-01 11:12:22.314 INFO (MainThread) [supervisor.resolution.evaluate] Starting system evaluation with state startup
2025-04-01 11:12:22.315 INFO (MainThread) [supervisor.resolution.evaluate] System evaluation complete
2025-04-01 11:16:16.561 INFO (MainThread) [supervisor.api.middleware.security] /supervisor/logs access from core_ssh

Most important error:

2025-04-01 11:09:32.966 ERROR (MainThread) [supervisor.homeassistant.core] No Home Assistant Core response, assuming a fatal startup error
2025-04-01 11:09:32.967 ERROR (MainThread) [supervisor.core] Can't start Home Assistant Core - rebuiling

And many warnings that add-on’s had timeout while waiting for addon to start
In this case HA did eventually start, but not all add-on’s did start. I entered a “ha su repair” command and after some time everything seemed to start this time. In other cases after 45 minutes HA still did not work.

My question is how can I best debug this issue? Which logs should I look at? Should I have used “ha su repair” or should I have waited longer?