Oh my. That IS confusing! So far, everything has auto completed for me, if I already had more than the required amount in inventory.
But since you only need to collect 12 more sands, hit up a few ponds before doing any upgrades and you should be fine. Once it's checked off, it's completed and it won't go back to 0.
Question: Are you asking about Beating the Sands of Time Part 3?
Mine says Slay 10 Nagas
Journey to the desert 25 times and have ?? Desert silks. (Idk how many because it auto completed)
Could it possibly be 12 more silks that you need?
Or, are the sands for Desert Flower Part 5 (I'm not there yet)
Either way, once it's checked off, it won't revert to 0, just make sure it's checked before using any of that item.
Good luck!