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I've had a look at conditional indexing but I'm not convinced its the same use case. As far as I can tell its a permanent selective index whereas I want temporary one (in other words I want to reindex just one customer). The big problem is that if I want to reindex one customer I cannot take them offline without taking all of the other customers offline too. Since it can take > 1hour to reindex we are starting to get concerned!
We are currently working on implementing sharding so we might have more information soon.