As a matter of policy, Zencastr won't delete files from your dropbox account. However, sometimes these files get moved, misplaced, or deleted by accident. You can recover them easily using Dropbox's web interface.
Make sure you are logged into the same dropbox account as you connected to Zencastr and navigate to dropbox.com/home/Apps/zencastr. Here you should see a folder for each of your projects. If you drill down into the pertinent project then you can start the recovery process.
Near the top of the page there will be a small trashcan icon. Click on this and it will allow you to see and opt to recover files that have been deleted or moved.