The new profile page has the wonderful new function to hide communities. But, as I can see, they are removed only from the new profiles — not from the site profiles still using the old profile page, and also not from the network-wide account page.
It seems to me as if the new profile page would be somehow an isolated part of the SE software. Is it an intentional feature?
From the viewpoint of the SE users taking part in multiple communities, the best solution would maybe be this:
- if the site icons belonging to hidden communities didn't appear in the combined flair,
- but they would be still counted into the combined reputation.
From the other side, maybe you won't confuse things (especially with this mixed flair behavior), and try to isolate the new profile functionality, at least in its currently newborn state.