You cannot change the color. But you can have WinSCP select (highlight) the different files.
Go to Commands > Compare Directories.
See https://winscp.net/eng/docs/task_compare_directories

Hi Folks

I'm a long time user of this excellent software. I'm now using it more and more with various web-projects and need some help with 'setting colours'.

I'd like to give files a particular colour when their date-stamp is newer than the version on the website. Is this possible?

Thanks

Steve