I am successfully getting Fluent NHibernate to update my database by calling UpdateBaseFiles:

Public Sub UpdateBaseFiles()
    Dim db As SQLiteConfiguration
    db = SQLiteConfiguration.Standard.UsingFile(BASE_DBNAME)
    Fluently.Configure() _
            .Database(db) _
            .Mappings(Function(m) m.FluentMappings.AddFromAssemblyOf(Of FluentMap)()) _
            .ExposeConfiguration(AddressOf UpdateSchema) _
            .BuildConfiguration()
End Sub
Private Sub UpdateSchema(ByVal Config As Configuration)
    Dim SchemaUpdater As New SchemaUpdate(Config)
    SchemaUpdater.Execute(True, True)
End Sub

How do I output the DDL to a file, I do this when initially creating the schema by using:

Private Sub BuildSchema(ByVal Config As Configuration)
    Dim SchemaExporter As New SchemaExport(Config)
    SchemaExporter.SetOutputFile("schema.sql")
    SchemaExporter.Create(False, True)
End Sub

but SchemaUpdate does not have a SetOutputFile method.