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I think the main thing to clarify here is the exact billing meter the Database Savings Plan is being applied to. Azure SQL Database and SQL Server on Azure VMs can have different eligible charges, so it would be helpful to check the Savings Plan details and the Cost Management breakdown for the affected subscription.
Also, SQL Server licensing through Azure Hybrid Benefit is a separate consideration, so I wouldn't assume that a Database Savings Plan automatically covers every Enterprise licensing charge. Microsoft should be able to confirm which specific meter is being covered before another plan is purchased