You say you need to authenticate the users using client certificates. I assume that this does not mean that the FTP server requires it.
The FTP protocol is implicitly file based (hence the 'F'). It only knows about files. You would need a client that had been modified (ok, hacked) to make the server believe it was getting a single file, while it was actually getting the data from the other connection. If the existing FTP server host is something you can modify, and you can run something like xinetd, it would be pretty easy to "roll your own" application to accept and store files.
If you're stuck with FTP, but have the ability to have programs run on the FTP server (like via cron), you could file-buffer, eg filename.10meg.1, filename.10meg.2. You could write these files sequentially using FTP, then have a cron-based script look for filenames in this format and catenate them together after-the-fact.