This is an incredible help. 
i do not actually think we will be using the inventory module here, it isnt complex enough for our needs. So I am trying to figure out how to undo this madness so that the P&L is accurate. 

do you have any ideas?

i was going to deactivate all inventory items. Make adjusting journals to ensure the right amounts are in cogs/revenue accounts and just upload all items as non inventory, since we are looking into an outside inventory management software. 

Would moving the quantities to positives undo these COGS decreases? Or is the method I am thinking the only feasible one?