How do I keep FTPSync from deleting the destination files in a directory that I have excluded?

A general rule is, that FTPSync takes care of files it transfers. So, if you transfer files with one .INI file, and then exclude a directory in that .INI file, FTPSync will remove the directory/files.

 

You should now create a separate .INI file for transfer of your excluded directory and transfer them using this new .INI file.

 

After that, transfers done with first .INI file, will no longer transfer/remove your excluded directory. But you should now never remove the ExcludeDir from it, because if you do, this first .INI file will again become "responsible" for this directory and will remove it, if you add ExcludeDir again.