This week I was using Flask-Migrate to do a database data migration. I created an empty reversion file and put my migrate script in it so that the migrate can be recorded just like the other reversion files.
The only thing special about writing a migration script is you need to use raw SQL to do the database manipulation instead of using ORM model object from Flask-SQLAlchemy. The reason is that maybe at the time your script is written, your model definition in your application reflects your actual database structure, but it may change over time, and once that happens, your script may not work correctly anymore.
This is one thing that I think is quite important when you are doing data migration with Flask-Migrate.