You might consider using our Remotely Hosted Downloads feature, which is available with our subscription plans starting at $18/mo and up. With this feature, rather than uploading files manually through our Seller Admin, you could simply configure each product with a Remote Product File URL pointing to a file stored on your own server, so you could simply keep the files at your end updated to the latest versions.
As long as the remote file URL (including the filename) remains the same for each product, our system will detect when the file at your end has changed, and we otherwise employ caching to minimize unnecessary file transfer bandwith usage whenever your remote file has not changed. The unique download links we issue to each buyer would cloak your remote file URLs and otherwise enforce your products' link expiration settings. This help page section explains in more detail how this feature works:
http://www.e-junkie.com/ej/help.file-downloads.htm#remote
