The only thing that concerns me is; since the remote panel does not automatically refresh would Winscp still transfer the generic word doc from my local machine to the remote one since it would appear that the generic word doc is already on the remote side when actually it has been removed by the script on the remote machine?
Remote directory is refreshed only after some operation (like file upload). However if new version of local file is created, it would have newer timestamp that obsolete version in remote directory. So WinSCP would consider it appropriate to upload it again.