Could WinSCP have an option - rather than using modification times or file sizes - to use a sha1/md5 hash of the file to determine whether it has changed? This doesn't reveal which direction to transfer the file, obviously. Maybe then m-time could be used, or the user prompted.
My request originates out of frustration with synchronization and Daylight Savings Time. I have a number of large files that are identical but whose m-time is off by exactly 1 hour between the source/destination. I don't want to rely exclusively on the file size comparison because contents of these particular files may change without changing their size. I'd like to ignore the m-time difference if, in fact, the files are the same (as a hash would reveal). If the hash is different, then the newest m-time would reveal which direction to transfer the file, or I could use the preview feature to set the correct direction.