Trunk will track that it's been deactivated but it won't mark it as out of stock. That's because we don't know why you deactivated a listing in the first place. Perhaps your intention was to deactivate it on Etsy temporarily while you fixed its description.

If you intended for it to be out of stock, you should instead adjust it within Trunk or on your other sales channels so that Etsy will then be properly synced to be deactivated and out of stock.