Seems that the addon doesn't work after the patch today, gives no warning or anything. But there is no communication between sub guilds.

Well, it looks like it's one of two things. From the patch notes

UI

BattleTag™ or Real ID friends are now only able to send 10 chat messages every 10 seconds over Battle.net® chat. User Interface Add-Ons should use the new send function and receive events to send communications information.

and/or

There's a hotfix that's currently being worked on to allow UI add-ons to send and retrieve Battle.net® friend invite notes.

But there's nothing I see about an addon send communications to a custom chat channel inside the game. And that's where it's broken.

If I type in a message directly to the hidden chat channel with the correct format, it will be echo'd out to all the co-guilds except the one I'm in.

C#audacia##Test Message

Will go out to all the co-guilds except AIE Audacia.

Hrm.... doesn't seem like the co-guilding would have been broken

That's my concern. There shouldn't have been a change in how an addon writes to custom chat channels.

Ok, from what I can tell, the problem is in that the "send guild message" ("CHAT_MSG_GUILD") is not firing. I'm seeing all the other events hapening in the log, but not chat messages.

The change in 5.4.7 is that the sender passed to the chat event handlers now has the realm name appended even when the sender is on your realm.