So how does the system deal with someone entering at an ungated station to exit at another ungated station, carrying a pre-paid card with a zero balance? If gripped it seems the RPI won't be able to tell whether or not they touched in and whilst the overnight reconciliation would try to charge a maximum fare for an unresolved journey but this would be declined due to the zero balance.

It is a bit theoretical though, as I doubt there's enough potential ungated to ungated journeys that would make this a worthwhile bit of larceny.
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Roy