There are 3 areas in Quik Invoice that hold invoices. First, there are Active Batches. You post batches from this list. A batch is posted directly into Accounts Receivable. When the batch is posted, it is removed from the Active batch list. You can find the posted invoices in the Quik Invoice History file. Archive batches must be moved or copied to the Active batch area before they can be posted. If you copy a batch, it remains in the Archive Area and a copy of the batch is made available for posting. If you move a batch, then it is deleted from the Archive area after it has been created in teh Active area.

Is it possible you moved (rather than copied) a batch from the Archive area the last time you performed this function? The fastest way to get the invoices back would be to restore the invoices from the historical file.