When entering a debtor invoice, type in the product code: if it has been set to use batches, you will be shown a window with the available batches:
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Enter the line number of the batch to issue. In the example shown the user is choosing the 2nd batch.
The batch will be inserted at the end of the detail line in brackets.
You don't need to do anything else: the text in brackets will show the total amount available, not the amount you're issuing (which is in the quantity column of the detail line).
Stock is only reduced when you post the invoice:
Don't pfaff around with the text in brackets and don't use brackets for anything else on the detail line, or you'll muck it up- OK?
Don't post invoices with items that have batches by right-clicking and choosing “Post” from the invoice list, as the script won't run, and the stock won't be deducted.