Hi, Holiday,
The Invoices module doesn't really care if your new year batches begin at '1' or not. It leaves it up to you to make the decision, dependent on what your preferences are.
In Invoices, if you go into the Company Profile on the System Options tab, notice that this is where the 'Next batch number' and 'Next archived batch number' are specified.
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Regards,
Softrak Tech Support