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DynamoDB tables are truly only provisioned where a user needs to worry about the keys/Indices involved. My recommendation would be to delete the table, and re-provision it using a CloudFormation template for consistency.
I have a hunch that this customer is very used to classic relational databases, and doesn't have as much experience with NoSQL implementations like DynamoDB.
I would consider tuning IAM permissions for the application to not allow deletion of the table itself to protect against accidental total deletion.
Additionally, I believe it is possible to create a CloudWatch alert that would fire on any deleted tables in a production environment.
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