How to prevent rsync replacing symbolic links with new directories in the target directory hierarchy

If you are using mac OSX aliases, then find . -type l won't come up with anything.

You can use the following [Node.js] script to move/copy the targets of your symlinks to another directory:

fs = require('fs')
path = require('path')

sourcePath = 'the path that contains the symlinks'
targetPath = 'the path that contains the targets'
outPath = 'the path that you want the targets to be moved to'

fs.readdir sourcePath, (err,sourceFiles) ->
    throw err if err

    fs.readdir targetPath, (err,targetFiles) ->
        throw err if err

        for sourceFile in sourceFiles
            if sourceFile in targetFiles
                targetFilePath = path.join(targetPath,sourceFile)
                outFilePath = path.join(outPath,sourceFile)

                console.log """
                    Moving: #{targetFilePath}
                        to: #{outFilePath}
                    """
                fs.renameSync(targetFilePath,outFilePath)

                # if you don't want them oved, you can use fs.cpSync instead

There's only one kind of symbolic link.

The issue you're seeing with FTP is probably that the FTP server is restricted to a subtree of the filesystem (this is called a chroot jail), and a symbolic link pointing outside that subtree won't work. That's by design: the chroot jail is for security, and you mustn't be able to escape the jail by following a symbolic link.

Arrange for all the files you'll ever need to access with FTP to be in the jail. Symbolic links will work as long as they don't try to escape the jail.

(If you are root on the machine, there are ways to make more files accessible within the jail, but I don't recommend fiddling with this if you don't understand all the issues.)