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You are correct in your understanding. Early retrieval charges for S3 Glacier Deep Archive are indeed triggered when the data (objects) is accessed, deleted, or changed, not just when interacting with the bucket or folder structure.
When you upload new files to an existing bucket or folder containing Glacier Deep Archive objects, you will not incur any retrieval charges on the existing files. Adding new objects to a bucket or folder does not affect or trigger any operations on the existing Glacier Deep Archive objects.
S3 Glacier Deep Archive has a minimum storage duration of 180 days. If you delete, overwrite, or transition objects in this storage class before the 180-day period is over, you will incur a prorated early deletion fee for the remaining days. However, simply adding new files to the same bucket or folder structure does not count as modifying existing objects and therefore does not trigger these charges.
You can safely set up a bucket with nested folders and continue to add new files to it without worrying about incurring retrieval or early deletion charges on existing Glacier Deep Archive objects. This approach is perfectly fine and won't cause any unexpected costs related to your archived data.
Remember, charges are applied at the object level, not at the bucket or folder level. So, you can continue to use your existing bucket and folder structure for organizing and adding new files without concern for triggering charges on your archived data.
Sources
Understanding S3 / Glacier Deep and is it safe to delete | AWS re:Post
Understanding your AWS billing and usage reports for Amazon S3 - Amazon Simple Storage Service
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