If you add a missed invoice BEFORE a Take Inventory that you have already done, S2k will auto correct the existing Take inventory after that date. Here is an example of how this works:
Below is an invoice that was changed AFTER a take inventory was taken:
Here we changed the quantity of the invoice for 2 items from 5 to 10 each and here is the revised take inventory invoice:
And you will see that the Qty in Stock has changed as shown below – this is the before the Take Inventory report: