I'm using Ararat Synapse for Delphi, so if there's a way to set such a mode (or get ls results to a stringlist) I can do it with code. I've looked at the unit code and the dokuwiki and haven't found anything conclusive.
But if there's an FTP command or setting I could use to prevent overwrites (resulting in a GET or PUT not being performed) it would save me a lot of time.
The only way using normal FTP commands that I see right now is to put each file in a folder. Before creating the folder I try to CD to it and PWD the current directory.
In other words, a sort of "sync folders", but only for a specific list of file names.