Picking up a chest can corrupt the inventory slot in which it was picked up. Corrupted inventory slots cause certain item types disappear when placed in the inventory.
When using LookUp Anything to check their numbers the number was not reduced, as if they were being sent to a hidden chest.

Saving and reloading the game will restore the corrupted slots so items disappearing no longer happens, but lost items will no longer appear for LookUp Anything, they will be completely lost.

I have also noticed that picked-up chests sometimes appear with a stack number as if they had items inside, even if they are empty. I am not sure if this bug only happens when that happens. After reloading the items count goes back to 0.

Disabling any mods that alter items or inventory like expanded storage, space chase skills and items or chest anywhere did not prevent this behavior, I narrowed it down to Better Chests.

https://smapi.io/log/51b2c92a2a5749c38e9d52c861981708

Edit: Items having their Edibility set to -300 was caused by another mod. Being an information/automation mod I didn't think it touched items. Turns out it's bugged and prevents eating by changing edibility instead of intercepting the eating process, without revering the edibility back afterward.

The other issue may still happen. But it's so rare I cannot replicate it on demand. It has not happened yet when Better Chests is disabled, so I had to narrow it down to Better Chests or its dependencies. It may take a whole lot of time to happen, like leaving the game running all night.

An update on this. Repeatedly picking and dropping chests around the farm resulted in the appearance of a mysterious "Chest #1" that cannot be found anywhere on the farm. This chest appears in the list of Chest Anywhere, but not in the Better Chests list, even when set to show all chests in the World.

对此的更新。反复拾取和放下农场周围的箱子会导致出现一个神秘的“箱子#1 ”，而这个箱子在农场的任何地方都找不到。这个箱子出现在“随处可见的箱子”列表中，但不在“更好的箱子”列表中，即使设置为显示世界上的所有箱子。

I also have this problem, but I found the reason, it's because you have an empty treasure chest and store it in a certain treasure chest.
【An extra mysterious treasure chest】【Like this, and cannot set】