I would class that as an outside event that is not under the control of the clock implementation. However, even in that case, the clock knows a second has elapsed. It just couldn't do anything while it was suspended.
Very few timer implementations guarantee exact delivery of events, but we don't consider that as being inconsistent with tracking time. That's just the reality of non-real time systems.
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You're talking about delivery, not the definition of a second. The definition of hour is dependent on the specification of the clock. A second is a second.