When you extract the Archive.zip file on a Mac into an existing folder structure, you may need to hold down the Option key so the folders in the Archive.zip file merge with the folders already on your computer. If you do not hold Option, macOS creates a new folder when a folder with the same name already exists.
For example, if you already have a folder for ABC Pty Ltd because you previously processed and downloaded documents for this client, the next time you process documents and extract the new Archive.zip, you must press and hold the Option key. This displays the Merge button, allowing the contents of the existing ABC Pty Ltd folder and the ABC Pty Ltd folder inside the Archive.zip file to merge.