The inventory is designed to be fully customizable, that means you can add, edit and delete everything.
If you delete an item, you actually remove it from your personal list of ingredients. When organizing inventory stock amounts you don't want to delete items, you want to edit the inventory amount field (setting it to 0 indicates out of stock).
If you accidentally delete an item you can add it back by either: 1. Add it back from a recipe where the ingredient have been used from recipe (preferrably), 2. Add it again filling in the info manually, 3. restore default data in the settings (warning: this will reset all in the given category).
You substract from inventory when you plan a batch, and actively check each ingredient to remove them from inventory.