that behaviour cant be explained.
your dashboards dont even know the token from appdaemon.yaml if you use the default widgets.
and HA doesnt know that dashboards are from appdaemon.
that can only be explained if you got a custom widget that somehow retrieves the token from appdaemon.yaml
but like i explained before, there are also race situations. so it is probably just coincidence that its not there after you added the token.