Hi John, firstly, the outcome you’ve described is, unfortunately, correct.
With regard to the impact on your FY20 tax payments, are you a provisional taxpayer? If so, presumably the provisional tax you have already paid will meet a good proportion of your FY20 liability and you will have a final instalment due on 7 May. In connection with this payment, the IRD has advised that it will write-off penalties and interest in late payments. It doesn’t remove the obligation, but it does mean you can defer payment. No time is specified, but you might perhaps take it to the end of the 12 week subsidy period? If you are not a provisional taxpayer, the additional tax will flow through to your terminal tax payment due on 7 July (or 7 April next year if you have a tax agent). At this stage it is not clear if the IRDs willingness to write-off penalties and interest will extent to payments due in July. One hopes things have improved by then… The double whammy is that, if you are a provisional taxpayer, your payments for FY21 will prima facile increase also, but you can estimate down so you only pay based on expected taxable income. All the best.