Hi Edward,

What version of Ledger is being used?
Does the Ledger data pass an integrity check?
When printing/previewing the batch status report, with all statuses selected, what is the status of the batch?

The way to remove batches from the control files is to print and purge the batch status report, as you are doing. Unpurged batches from this report would typically be due to corrupted data, or the batch wasn't selected to print on the report and thus was not cleared.