I tried starting my old game after downloading update 7, but (as I expected) was still not able to obtain empty gourds. So I started a new game and now I have a couple of empty ones already. Yay!! :D
That's interesting. I don't think that is the issue here because I think the items were not actually missing. It looks like they were just in the extra inventory slots that you have to scroll down to get to in the inventory.
I'll keep the serialization in mind if there are any issues with items or the inventory in the future.
I believe I have found the problem. I tried everything I possibly could to reproduce this bug with a full inventory: crafting while the inventory was full, breaking down stuff and salvaging in a full inventory and harvesting with a full inventory. The extra items drop out of the inventory as expected and you just have to pick them up again when you have enough room.
However, upon watching your latest youtube video I noticed something peculiar. You seem to have missed the scroll bar on the right side of the inventory and think that your inventory is full when it is only half full. Scroll down in the inventory by dragging the scroll bar or use the mouse scroll wheel. You should find your missing items in the 4 extra rows of inventory slots that you have :D