I am also having the problem with the storage chest vanishing after reloading a save. I have no problem opening CoCED with 1.4.16d, and I confirmed in there that the desert chest flag is set.
However, once you obtain the weapon, shield, or armor rack you are able to access the storage tab again, HOWEVER, you are unable to access the generic storage chest. Attempts to put anything in it just simply fail, and there is no button to remove anything placed inside originally. The storage tab remains after obtaining the weapon, shield, or armor rack and loading your save.
Removing the chest and then obtaining it again from the desert once again allows you to access it. Reloading a save breaks the chest again, however, but as long as you had one of the town ruins specialty chests you are still able to see it on the stash tab.
One further bug I've found with reloading saves: When you have an empty inventory, upon reloading the save you will find you have 3 ovi elixir.
Nothing in my inventory.
Inventory after loading the save game. Ovi elixirs in slot #4. I do not have 4 inventory slots normally at this point in the game, only 3.
As for the volcanic crag, it states in the release notes on git that the crag was removed, and the items you could find there are now found in the glacier. As for the Behemoth, he moved to the 'secret' dev room for now.