First off, thanks to everybody who's reported the disappearing stash when upgrading storage issue.
Obviously, we understand this is a really irritating bug and we appreciate how frustrating it is to lose your hard-earned items.
The good news is that the cause of the issue has been identified, and a fix is now going through testing. We currently expect this to be released early next week (although if any other issues come to light as a result of this fix and that plan changes, we will of course let you know).
Meanwhile, there is a workaround until the fix is in place - if you make sure to have your stash open while applying the upgrade, your items should be safe.
Thanks as always for your support and patience as we work through Early Access!