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If you can provide evidence (ie. Garmin track) that you rode the route then it should be ok. Not sure how much Nathan cares. I remember one of the racers in the first one I did not happy about one of the Italians who disappeared for days and he reckons there's no way they moved ahead. But I can sympathise with tracker issues too, having sent one faulty Spot back for replacement myself.
I'd forgotten about him. What's the rule, though? Can you legitimately finish if you haven't been tracked for so long?