Items disappeared from the inventory

I was finishing a map in Atlas when the server disconnected, and all the items I had collected on the map simply disappeared from my character's inventory when I logged back in.
Other people reported that the same thing happened after the server disconnected.

The instance on the server crashed, so you got rolled back to the last server save point, which is why the items were gone from your inventory.

Unfortunately there is nothing that you can do to prevent it. It is a good idea to return to town/hideout frequently to stash things - that should force a server-side save point.