Compare sub folders too?

[bigstar]

The "Compare folder content" feature provides a visual comparison of current folder content.

It is not intended to do anything more than that.

If your FTP server supports MLSD or you're using SFTP you can configure your file transfer rules to skip all files with the same date and then you can queue the base folders and only modified files will be uploaded with everything else being skipped; assuming of course you have the preserve date on upload set.