Objects in Amazon S3 are immutable. This means that be replaced, but they cannot be edited.
Amazon Athena, Amazon Redshift Spectrum and Hive/Hadoop can query data stored in Amazon S3. They typically look in a supplied path and load all files under that path, including sub-directories.
To add data to such data stores, simply upload an additional object in the given path.
To delete all data in one object, delete the object.
However, if you wish to delete data within an object, then you will need to replace the object with a new object that has those rows removed. This must be done outside of S3. Amazon S3 cannot edit the contents of an object.
See: AWS Glue adds new transforms (Purge, Transition and Merge) for Apache Spark applications to work with datasets in Amazon S3
Data Bricks has a product called Delta Lake that can add an additional layer between queries tools and Amazon S3:
Delta Lake is an open source storage layer that brings reliability to data lakes. Delta Lake provides ACID transactions, scalable metadata handling, and unifies streaming and batch data processing. Delta Lake runs on top of your existing data lake and is fully compatible with Apache Spark APIs.
Delta Lake supports deleting data from a table because it sits "in front of" Amazon S3.