What I have done in the past is used a lock file that is generated on the sending side and that you delete after proccessing the file.
For instance:

Empty ftp dir
Client connects to ftp server and drops active file (testfile.zip)
Client verifys ftp completed and puts another known file (testfile.zip
+.lock)
[download]

Meanwhile your application loops and does nothing until it sees testfile.zip.lock exists whne it then grabs that file and does something with it and deletes the file and the lockfile. The other side can be configured to check for the lockfile before it sends the file to verify that proccessing has been completed without clobbering data.

-Waswas