Hi, Kate,
Have you seen this behaviour yourself? Are you able to duplicate it in both the active data and in sample data?
If the missing invoices were being posted to customers for whom those invoice numbers already existed, they would not post. However, you would have received a message informing you of the duplicates and they would then have been placed in an error batch.
Could this be what happened? Could the error batch have then been deleted? Does the Batch Status report provide any more information?
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Regards,
Softrak Tech Support