If the migration has already been applied to the database it must be backed out before re-scaffolding (by targeting the previous migration with Update-Database).
Visual Studio for Windows (with the Azure SDK) provides some help in creating a table controller. In older versions of SQL Server, this was required to increase performance on the table as a whole.
Right-click on the Controllers node and select Add - Controller.... It may not be required now and may be removed in future versions of Azure Mobile Apps.
One way to do this is by tearing all the way down to Migration ‘0’, and the doing an ‘Update-Database’ to bring it current. Learning Migrations can be a frustrating time suck. Instead take a breather and relax, then come back to it.
It is an investment, but when mastered it will pay dividends to your team and process.
Visual Studio provides scaffolding for a new table controller. The dialog asks for the model (which is actually a DTO) and the data context (which is already created). There are a lot of times when the existing table is not suitable for this sort of schema adjustment.