You can use option failonnomatch on to make WinSCP return "error" exit code 1, when there's nothing to synchronize.
https://winscp.net/eng/docs/scriptcommand_option#failonnomatch

I use WinSCP to sync down a folder and then use a Windows Batch file to process it.
Is there any way to flag when "Nothing to Sync" is present so that I can just tell my batch file to move on to the next if there is nothing to do?

Normally, I'd just check for the existence of files and move them out of them from the download folder between runs but in this case I can't change the files on the server so I have to use other methods to tell if the files are new.