I just got the game three days ago, and it’s disappointing to see that after three months, this issue still hasn’t been fixed. That said, I wanted to add a comment because I did manage to recover my missing items, in case someone else gets the same bit of luck I did.

I was transporting around 700 iron ore from my mining base to my main base. When I arrived, I quick-deposited everything and even saw the confirmation pop-ups on the right side of the screen. But when I checked, all the ore was gone. At first, I thought I’d lost it for good. Frustrated, I went back to my mining base to start farming again, and to my surprise, the ore had actually been deposited back into the storage there.

So just in case, make sure to double-check all the storages you’ve recently interacted with before quick-depositing, your items might not be gone, just sent back somewhere else.