I was doing my first upgrades beyond level 5. I had enough materials to upgrade the privateer's vest once from level 6 to 7. Yet the materials were not removed from my inventory as long as I kept the upgrade screen with the vest selected active, allowing me to upgrade the vest all the way up to item level 10. Closing and re-opening the upgrade menu shows that only the costs for the upgrade from 6 to 7 were removed from my base's inventory.