Hi. Thanks for your reply. I have already read the faq link. I don't want to use synchronization with timestamps because even if it does not copy old files, it has to go through all the older folder and files and compare, which it should normally not take long but if we are talking about more than 2000 folders then it does take long to copy the new files.
I found a temporary solution where I use keepuptodate and I use Windows Task Scheduler to Start and End the batch file every 30 minutes so that it does not go through thousands of files all the time but only the ones created in the last 30 minutes. Maybe there is a better way to solve this using some WinSCP command but I have not found one yet.