I am successfully getting Fluent NHibernate to update my database by calling UpdateBaseFiles:
Public Sub UpdateBaseFiles()
Dim db As SQLiteConfiguration
SchemaUpdate
calls the action for each update it does so you dont want to be recreating (and therefore overwriting) the same file on each command as above, this is what is required:
using (var file = new FileStream(@"..\..\..\schema-update.sql",
FileMode.Create,
FileAccess.ReadWrite))
using (var sw = new StreamWriter(file))
{
new SchemaUpdate(config)
.Execute(sw.Write, false);
}