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I recently enabled Azure blob storage in Sitecore 10.3. If I delete a file from Sitecore, it is not deleted from blob storage. I deleted the item from Recycle Bin of Sitecore and I ran database blob cleanup as well.

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No, they are not deleted, not even orphan blobs. However, orphan blobs can be deleted from Sitecore XP:

(Control Panel => Administration tools => Database Cleanup => Database Name => Cleanup Blobs => Execute Cleanup)

For more details see the blog post: Sitecore Media in Database Vs. File Directory Vs. Blob Storage

What is the way to migrate existing media files that are stored in a file system?

Yes, you use the blob migration tool to help migrate blobs from SQL Database to Azure Storage and vice-versa. Use the blob migration tool

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  • what is the way to migrate of exiting media files that is stored in file system Commented Sep 8, 2023 at 14:22
  • I have updated the answer. Commented Sep 8, 2023 at 14:25
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A potential reason of this behaviour can be the "soft delete" setting in Azure Blob Storage. When it is turned on, Azure will not delete blobs immediately and instead will keep them for the specified retention period. This is useful for cases when a media file is deleted accidentally and needs to be restored.

You can check if this is enabled on your instance or not by going to Azure Portal, selecting your Storage Account and navigating to the settings under Data ProtectionRecovery. Find the settings Enable soft delete for blobs and Keep deleted blobs for (in days). Recovery settings

You may want to reduce the retention period to delete blobs sooner but I would not recommend disabling "soft delete" completely just in case you will need to restore accidentally removed or overwritten items.

Please see Sitecore and Microsoft documentation for reference.

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