The context.Metadata is just a copy of the real metadata that is passed to the context in the constructor. Your changes are not taken in account. Can you change the original metadata by overriding the
protected virtual void OnDatabaseOpen(BackendConfiguration backendConfiguration, MetadataContainer metadataContainer)
Method in you context? If your context is generated, just add a partial class with the same name and override OnDatabaseOpen and put your code there.
metadataContainer.UniqueIdGenerator.CreateTable = true;
metadataContainer.UniqueIdGenerator.TableName = "Sample";
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