If you should also encounter the problem that WinSCP's wonderful syncing / folder watch functionaity "Keep remote directory up to date" doesn't work correctly, first have a look here, also for troubleshooting: https://winscp.net/eng/docs/task_keep_up_to_date
I couldn't find a working fix for this, but I found a good workaround:
The problem for me only occured on SSH connections, so simply switch to SFTP and it may also work for you ;)