New Zealand Law
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The manager has the power to bind his employer, and if you were told there is no charge for the services, then they are bound by this. If the owner suggests otherwise, you have a choice of either reaching a settlement, or of disputing this somewhere like the Disputes Tribunal and you would have a defence to any claim by saying that you were told there was no other charge for the services. But the owner cannot unilaterally decide that there is to be a charge, once his manager has decided to waive any charges.
It seems a bit unusual the owner is chasing a bill which I assume is at least 20 months old, and likely to be much older. The fact you have cleaned out records is why that makes his position a bit weaker but in the end it may come down to your word against his, and the delay will weaken his position