Ok, we have a hub, and about 20 bots connecting to it, most of which are in different channels. Some users are ops in more than one channel. Most of the bots share user records.
I was talking with another owner, and he said the hub has to be in all the channels the leafs are in. Well, not "in", but at least have a channel record of them (set to +inactive) or when the bots share userfiles, the leafs will get overwritten by the hubs, and lose the user information for the channels the hub does not know about. I thought I have done this before, but it is very possible I am mistaken.
The hub will accept data regarding flags for channel it does not know about.
However, it will discard this information, as it has no use for it. This is the same for a leaf. A leaf will discard incoming details about a channel it has no need for.
So yes, to get the hub to remember, you will need to set the channel in the hub, and make it +inactive.