You think you can police an ftp upload area in a day, you must be kidding yourselves.
Its needed for the server operator to put in place a tool that can catalogue ever archive on the ftp. As is now and for nay new archive upload automatically. And leave a log of the contents in a file beside each archive file checked. Now all that is needed is for you to read the contents file list to know what is in each archive.
Next if an archive has some software or file not agreeable to be the ftp. You will have to download that archive remove the files. and reupload the archive back to the server.
Can the ftp have an automated tool to do this, it will make for managing the ftp easier. It'll be the only way to do it easily.
The upload zone is no special place just another folder. So no special upload pass needed to upload their. Uploaders upload to their own folder. This will make for sorting new files to the ftp easy also, into correct folders. Easier for managers because the archive have allready an automated archive catalogue that ftp made for it.
Remember don't delete archives because you cannot be bothered to download, remove files and reupload. If you feel that your likely to this then don't bother to be a ftp manager, we don't need you.