Here are some options on how to update objects that are not updated by the update model wizard (based on your scenario where a the column definition was altered): The best option would depend on the given scenario.For example, if you just altered the definition of one column, then option 1 is likely you best choice.
For example if I change a field from non null to nullable or if I remove fields the update model does not reflect the changes.
I have had to remove the entity and add it back in to get the changes to appear in my model.
Install all components and restart, now you should have mysql server running again but now you will need to migrate the old data to the new.
First up make sure mysql is not running either from System Prefs or the Terminal.
The Update Model Wizard also makes some changes to the conceptual model and mappings, but it only makes these changes when objects are added to the database.