Yes

You need to do a retroactive inventory adjustment to create enough stock at the beginning of the invoice list so that the subsequent invoices can sell those items without going negative.

If you have not already done so - run an item sales report for the period in question so you get a list of the items & qnty needed.  You will also need to determine what the average unit cost of eash separate item was at that time - since the inventory is not in QB you will have to figure that out yourself.

It sound like the value of your stock was on the books somewhere - presumably in a current asset account. So when you make the inv posting that account should be where the 'adjustment' goes.

Caution - if this problem goes back into the prior fiscal year and that year has already been closed then you probably should split the list and only change the portions related to the current year. Then review with your new CPA.