At times, on our estimates we throw in certain small dollar items for no-charge. We will create the estimate, select the inventory item on the inventory item listing and just zero out the "TOTAL" column to remove the charge and it would leave the "QTY" # intact (i.e. 1). Then when we converted to invoice/sales order - the item would be removed from our inventory on hand when sold. Just recently, something has changed in our system and when we remove the $ charge in the "TOTAL" column from our estimate, it automatically is reducing our "QTY" on the estimate down to zero. This is causing an issue as our inventory volume is not reduced by the sale and therefore inventory is overstated. I don't know if it has anything to do with the "Don't print items that have zero amount" box on the Jobs & Estimates company preferences but I don't see anything else that looks strange? I don't think we changed anything - not sure why it is operating differently now.
Thanks for taking the time to reach out to the QuickBooks Community for support.
To clarify, is this only happening when using an estimate? If so, it sounds like your template might be broken. Over time templates can get damage in them and create issues such as the one you're having with your qty. Let's create a new template and use it going forward. I've included some steps below to create a new estimate template.
Go to Lists at the top menu bar to select Templates.
This will open a page that shows all custom templates added to QuickBooks.
Scroll down to click the Templates drop-down and pick New.
Choose Estimate in the Select Template Type window and hit OK.
On the Basic Customization screen, tap the Additional Customization.
Then, click the Header tab to select Other and enter a name that will identify the field box.