The new nav menu does get a flag icon like this when there are new flags
though once you open your notification menu, this is considered seen and goes away — is the problem that the moderators are missing the persistent flag count?
There’s no way to get the count back with the new notification menu, the new menu will eventually be the default along with the sidebar, which is where the persistent flag count was relocated…
We’ll have to discuss this some more on our end, I’m not sure if we’re going to support Discourse without the sidebar long enough to warrant adding a count back elsewhere.