This is what you asked: "I need to fix the negative numbers that are currently in the "total quantity" column of my "Item List". "

And the point is, to figure out What is the Right Fix. That condition exists because you sold something you never bought. You need to Fix it for what Broke. That is either Populating the items that should have been on hand. Removing that what you sold wasn't really What you sold, or some mid-point that results in the correction you need.

This is not the fix: "and to convey that the problem leading up to the mistake had been fixed"

That is Preventing the oversight that allowed this to Continue.

"Not to mention it's contradictory - first you state I don't have to track it then go on to tell me how to track it. Our inventory is tracked through a different program"

Okay, that's a detail we needed and all we can do is describe things that Matter, in general. That helps you tell us your Specifics.

"and the appropriate entries are made at the appropriate time. No one is "just throwing values at the data". I don't need QB to track the inventory."

Exactly! What you have is a Periodic Inventory Management operation, then. Yes, you Throw Values "periodically." And yes, you Avoid using the Inventory Items in QB, which was the error.

"You then seem to think I needed to know how to fix the invoices because you state "Perhaps they also had a Noninventory Version of what they sold, before you arrived. Or, they used Service items. Look at older sales, to know what they listed in the past." Already did that, that is why I stated that procedures had been changed."

Remember, we cannot see Your File and we don't know what existed earlier. And yes, we peer users are trying to help with things we cannot even See. We tell you the same things we would be doing, if this file was in front of us to work on.

"You then quote my question back to me and never actually answer it.'

Well, yes, I did. I described the Various ways things go wrong, and Which and Where you control what needs to be controlled to make the Fix for the existing data.

Periodic Inventory management: All purchases are posted directly and generically to COGS or to Asset First. You never told us Which Is In your File.

Then, Periodically, we take a physical count and compute cost basis for what still is on hand, or get that info from a POS or "our other system" and Rebalance, by using a Journal Entry, between COGS and Asset, for what still is on hand and the basis or cost.

And that means Your Fix, is as follows:

Yes, you would Edit your Invoices and change them to using the Normal Sales or Charge item, which in your case is either Noninventory or Service or Other Charge (you didn't tell us what they Used to list for sales). That will remove all the chaos.

And Yes, this will take a while. But the work really is about the same amount of work: Adjust inventory item names when you never had inventory to start with, means also doing this by date Batches, to match to sales and avoid sales running negative. That is a Lot of Work, too, so fixing the invoices and sales receipts fixes Everything: Stops the inventory items from even being in use on the sales, removes the Computation that attempted to handle Average Costing and false COGS and negative quantity and removing asset when the Item was never stocked, to start with.