Batch Orders are intended to happen AFTER the orders included in the batch have been ‘Invoiced Matched’ already. Meaning that these costs are supposed to be final before you batch them. However, yes its not perfect world and sometimes mistakes and changes are going to happen.
When you Batch orders that have been invoiced matched, it marks them Paid. If you have to make changes after orders have been batched, then you have to Reset and update BOTH the original (ie VIC) order included in the batch order (so it recalculates the student funding) AND the batch order itself (so it recalculates the batch receipt). IMPORTANT: After resetting, modifying and updating both orders you MUST make sure to mark them both as PAID. If you leave the original (ie VCI) order at invoiced matched (or processed) it will again appear in the batch console to be Batched again.