Reflux stores don't play nice with webpack Hot Module Replacement

If have simple application using Reflux and everything works properly. I'm using webpack to build and run everything with HMR support. The react components get hot swapped properly and also the Actions and Stores get hot swapped. The only problem is the 'old' Store is still active and still reacting to the Actions. So every compile that changes something in a Store, you end up with another version of the Store.

Is there something that can be done to fix this?