@krissenior 

If you're in the process of just "considering" an alternative inventory app, I would strongly suggest taking a physical inventory count of the items of concern and updating them in QBO using COGS as the adjustment account (New > Inventory qty adjustment) so you're in control of the adjustments.  If it's not too time/cost-prohibitive, taking a full physical inventory is obviously the best.  IMO, the adjustments that QB is making is correcting your P&L so you may not be in as big a mess as you think.  Until you have decided on what inventory app to use, you will want to keep QBO inventory active and accurate so that you can transfer your inventory from QBO to the inventory management app and keep accurate inventory/COGS data until the switchover.  Just my $.02.