I'm not sure if this is different with sqlite but with postgres and mysql, you would do the following:
1) delete all the .table files in the databases directory
2) set migrate=True and fake_migrate=True (also make sure lazy_tables is False)
3) start your app with the scheduler option enabled. You should see the new .table files created for all tables in the db, including the scheduler.
4) shutdown your app and now you can set migrate=False (avoid any unplanned table changes) and lazy_tables=True. Now restart your app and it *should* work as expected.
This is how I moved quite a few of my apps between servers (all on postgres though - but I imagine it works the same with sqlite).
HTH,