We were unable to reproduce this problem.  Is it possible that you are running old code?  Here is an excerpt from ~/_controls/EditLineItemsView.ascx.cs that suggests that we are handling the issue properly.

That is a tricky one.  In my tests, I was saving the duplicate before deleting the line items.  The bug only appears when you duplicate and immediately delete.  The solution is to note delete the original line items if this is a duplicate operation.  We had to fix Invoices, Orders, Quotes and Payments.  The fix will be in the next build, or you can request the updated files directly from our support team.

Here is a sample fix for Quotes.  Please keep in mind that we also saved the DuplicateID into the ViewState for the specific purpose of checking during the save operation:

// 06/17/2008 Paul. If this was a duplication operation, then don't delete the original line items.
Guid gDuplicateID = Sql.ToGuid(ViewState["DuplicateID"]);
if ( Sql.IsEmptyGuid(gDuplicateID) )
{
   foreach ( DataRow row in dtLineItems.Rows )
   {
      if ( row.RowState == DataRowState.Deleted )
      {
      // 05/26/2007 Paul. In order to access values from deleted row, use DataRowVersion.Original, 
      // otherwise accessing the data will throw an exception "Deleted row information cannot be accessed through the row."
      Guid gITEM_ID = Sql.ToGuid(row["ID", DataRowVersion.Original]);
      if ( !Sql.IsEmptyGuid(gITEM_ID) )
         SqlProcs.spQUOTES_LINE_ITEMS_Delete(gITEM_ID, trn);
      }
   }
}