In facts, when you update a cook component, you have to make the database changes manually.
I know it is a little bit boring, but cook is missing this feature.
It could be a feature that take snapshots of the database structure in order to create the versions updates.
Lot of work, but half is already done because your dataset snapshots contains the database table, so cook could reuse that and step with versions.
Another possible cool feature.
I know you have solved your problem, but for others users, in case you have multiple installations, it is recommended to make a SQL version file.
Your cook component can manage such updates, look at the Joomla documentation to understand how it works.