I was in the same situation. Available updates to the HomeAssistant components (Core, Supervisor, OS) were not showing in the settings tab at the top where usually all other updates (add-ons, HACS, etc) are shown.
The issue can be resolved when going to Settings → Devices & Services → Home Assistant Supervisor → Services. Here select the entity (Supervisor, Operating System, Core). In the new window click on the Configuration/Update entity and select settings/cog wheel in the pop up window. Toggle the visibility and updates will once more show up at the top of the settings page.