Abstract: The current document is directed to methods and automated systems for handling files and other data during a data ingestion process that may contain PHI within the file content, filenames, file-associated metadata, and other such data-associated information. The methods and automated systems protect sensitive health information using encryption methods to prevent the protected health information from being exposed. In certain implementations, the currently disclosed automated system includes a client-network system, one or more client servers, an encrypted data-storage device including a source folder for temporarily storing original files downloaded from the client network system and a second folder for storing PHI-free files created from the original files, and processes that create the PHI-free files from the original files, remove the original files from the source folder, and securely copy the PHI-free files to a secure file-transfer protocol server to be processed for later use.