Hi Acrylon,
If there is a prepayment and an invoice with non-zero Current amounts that offset to zero, and you don't want any accounting entries to be generated, you could create a manual check entry and apply it to both the prepayment and invoice. Make sure the entry is set not to print. Posting this manual check entry will set the Current Amounts of both to zero and allow Period End to clear them to Transaction History, without creating any GL activity.
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Regards,
Softrak Tech Support