It’s recognised that it may sometimes be necessary to delete old versions and replace them with new ones (e.g. if URLs have changed).
The second option is just to overwrite the files. As long as updated files have the same URL as the existing files, uploading these new files will just overwrite the old ones. As the data should be cumulative (e.g. if publishing every quarter, the new files will include the quarter being reported on, and the previous quarter reported last time, and so on), this will just serve to add the new data to what is already there. It will also enable amendments to be made to existing data.