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Subject : I have MySQL Server contains Magento's DataBase (I have the diagram standard of magento) By VBA Excel I developped an application which extract many informations from Magento (By exécuting SQL requests). Question : Is the structuring of magento can be updated ? like there is a table called 'sales_flat_invoice' and after updating it will be called 'sales_flat_invoice_V2'

so if it is possible it means my application wont work anymore with old SQL Requests and I have to change the SQL requests in the application :( any help please !

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IN theory, the table names do not change.
It happened once in 1.4 when the sales_order table changed to sales_flat_order but this is because the sales entities were drastically changed.
But keep in mind that new tables may appear and new columns in old tables.

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