Yes, the functionality you're seeing is coming from the database... the Business Object Mapper uses the StrataFrame database to persist settings for your business objects. The Business Object Mapper has a project record that it ties to your computer through the full path to your project file. Since the project you re-created had the same path as the project you deleted, the Business Object Mapper thought that they were the same project and thought that it was already configured.
So, when you delete and re-create the project, if you want to delete all of the settings associated with the old project in the Business Object Mapper, you'll have to go into the project properties of the Business Object Mapper and manually delete the project configuration.
You'll also notice that when you move your project to a different folder (as is the case when you don't "save" the project when you create it and it creates the project in a temporary folder until you save it permanently) you'll have to "re-configure" your project through the Business Object Mapper. NONE OF YOUR SETTINGS WILL BE LOST as the Business Object Mapper's project record is not deleted, but you'll have to re-tie it to the new path for the project file.
Hope this helps

The "ghost" business objects Trent is talking about can also appear, just like he said, if the namespaces don't match on your business objects' files (half of the class is in one namespace, and half of the class is in the other namespace, and the Business Object Mapper thinks you've created two separate business objects with the same name, so it lists both of them).