I want it to be automated.
what precisely do you want to automate. can you describe the intended workflow?
is sicaries tip not the answer to your problem?
create a scheduled job in Windows that looks for that file and executes it when found.
regarding ssh:
Can this be done using secured login comand ssh?
if you install a ssh server on your windows machine then you can connect to it with ssh and you can execute console programs on the windows machine. it's been a while that i used that, but cygwin sshd worked well for me.
btw, an ssh server should relieve you from needing an ftp server (which, i beliebe, transfers the passwords in plain text, which is a bad thing) since you can use sftp,scp then.