Thanks to Martin Prikryl correction I was able to connect, here is what I did:
Created a text file with the winscp.com commands "connection.txt":
# Automatically abort script on errors
option batch abort
# Disable overwrite confirmations that conflict with the previous
option confirm off
# Connect with username and password
open ftp://username:password@host:port -implicit -certificate="aa:aa:aa:aa...."
# Change local directory
lcd C:\local_working_folder
# Force binary mode transfer
option transfer binary
# Download missing files to local directory from remote
synchronize local
# Delete all remote files
rm *
# Disconnect
close
# Exit WinSCP
exit
Now from command prompt or in a batch file you just call winscp.exe from where it is installed. If from installation media it should be C:\Program Files\WinSCP\WinSCP.exe of if extracted from a .zip portable version point to the folder where you extracted the file:
C:\WinSCP\WinSCP.exe /console /script="connection.txt" /log="conn.log"
Then just schedule the batch to automate the process.