You can use Session.FileExists and Session.RemoveFiles to check for and delete any existing file.
https://winscp.net/eng/docs/library_session_fileexists
https://winscp.net/eng/docs/library_session_removefiles

I tried this new feature today and I successfully copied files on our SFTP server. When I tried to copy the same files again I got the following message because they already exist in the target folder:

General failure (server should provide error description).
Error code: 4
Error message from server (en-US):

Common reasons for the Error code 4 are:
- Renaming a file to a name of already existing file.
- Creating a directory that already exists.
- Moving a remote file to a different filesystem (HDD).
- Uploading a file to a full filesystem (HDD).
- Exceeding a user disk quota.

I suppose I was expecting that DuplicateFile method would overwrite any existing file with the same name rather than error, but I can see why you have done it like this. Is there anyway to add a Boolean that if set will give me the option to overwrite, aka VBScript object.CopyFile?