You probably get a damaged file, but to be sure, you need to
know how your FTP server deals with such a case. I don't know
any FTP server that does, but it is technically possible to write an FTP server that doesn't serve a file that is open for
writing. Or an FTP server could first try to lock a file - if
the modifying program locks before updating as well, you're sure the downloaded file isn't mangled.
However, none of this can be influenced by the downloading program. The client doesn't know about files being modified.
Abigail