When an SFTP user is deleted from the web admin portal, the SFTP user's files will still exist in S3.
SFTP Gateway does not delete nor move (i.e. tombstone) the S3 location of the SFTP user's chroot directory. This is because SFTP Gateway leans heavily toward avoiding data loss situations.
If you need to clean up S3 files after deleting the SFTP user, this needs to be done manually.
Also, S3 files are not impacted when deleting a Folder from the web admin portal. Folders are just mappings or mount points. So if the SFTP Gateway Folder mapping is deleted, the underlying S3 files will still remain.
In general, actions in the web admin portal do not delete files in S3. File deletion in S3 occurs manually (e.g. via the S3 service in the AWS console), or via an SFTP client like FileZilla where the SFTP user has read/write access.