We have already lost some chests full of items, this is happening after the update, as we are on a PVE server there is no way anyone is stealing them, the chests are simply disappearing.
Better place them on ground. Things shelves disappear since ages. As well maybe check the decay time of every single chest placed on a shelf.
If it’s different to the base you can make a bug report with that.
You can try to see through the “Event List” what happened. If you find any irregularities you can also follow the stated in the Official servers guidelines to submit a ticket:
You can read the full version of the Guidelines here: