This is a temporary hotfix for shortcuts (including ⌘D) firing twice for some users on the first launch of 2.1.1.
If you accidentally deleted notes (sorry!), you can recover them via File > Recover Notes from The Void. If you're currently seeing this behavior, simply restart Antinote and it should be gone.
We're working on a longer beta period for releases so things like this get caught before they go out to everyone.