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The ECXpert FTP server is a custom ECXpert server that supports the 'submit' function (as well as a couple of other ECXpert specific functions). It is integrated as an ECXpert server. It can't be replaced within ECX but it can be replaced ("kind of...") by any ftp server: your remote client can use any FTP server, instead of the ECX server to deposit the files where a perl or shell script could 'submit' them. Or you could use the ECX FTP client to pick them up and submit them.
I seem to recall that ECX also comes with a slick automated FTP client that allows scheduling and supports SFTP.
In summary, if the ECX-packaged FTP server doesn't address all of your requirements, there are a multitude of options for submitting files that should help.