Cross index filtering

I've got a backlog of usernames. I need to pull data associated with those
usernames into a separate index.
I want a query that will let me do a terms facet on user counts in the
first index, with a facet filter excluding the users that already exist in
the second. Is there a simple way to do this?
There could end up being a couple hundred million unique users in the
secondary index, in theory. For that scale, what's the best way to approach
the problem?

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