How did I send 0 quantity to Amazon?

In SellerEngine Plus, if you manually change your Merchant Fulfilled quantities to 0  and then upload using one of the two options: Upload > "Add new items, remove items marked for delete, update existing listings" or Upload > "Update quantities for existing listings", The software will inactivate your listings.  This should not happen for FBA items as this is driven by Amazon through the API. 

Also, you can accidentally delete Merchant Fulfilled listings using SellerEngine Plus.  If any of your items have a check mark in the box in the "Delete from Amazon" column, this will completely delete your Merchant Fulfilled listing.  To prevent this, Highlight your whole inventory (CTRL A) then go to "Set Amazon Flags" in the toolbar, in this screen select "Clear Delete from Amazon".  This will make sure that your highlighted items will not be marked for Delete.