There seemed to be an update and now, there isn’t my logo, but the standard nextcloud-logo.
Nextcloud doesn’t auto-update (though AIO can be made to do so and some people do things with their Docker environments to make updates happen outside of Nextcloud itself), so you’d probably have some idea if you updated something.
Anyhow:
What version?
Is your logo still under Admin->Theming?
Can you provide a screenshot of the email so we know exactly which one?