Yummy won't navigate into Mac aliases or UNIX links when performing any transfers, synchs included. The reason for this is that it is all too easy to end up getting into a loop, where an alias points to a parent folder, since Yummy follows through all the directory structure. I guess that if you were very careful then navigation into aliases/links could be used in the way you have described, but currently Yummy doesn't support that and instead expects the local and remote directory structures to be similar, but not necessarily identical.
I'll see what happens if I allow this behavior in Yummy FTP. If it works out well, I'll add an option for it in the Preferences, but the option will be off by default.
