There's no simple way to solve this with WinSCP scripting.

You can replace your WinsCP script with e.g. PowerShell script with use of WinSCP .NET assembly.
https://winscp.net/eng/docs/library_from_script
https://winscp.net/eng/docs/library_powershell

With it, you can iterate the files and process then one-by-one doing any checks you need.

I am trying to move files from one remote folder to another remote folder. I am using the mv command and it works fine. The only problem is when there are old files in the destination folder (to be more specific: duplicates of the ones in the source folder), it does not overwrite (or simply skip) those files. The file i want to move still exists in the source folder. The remaining files in the source folder (other than the one that has a duplicate in the destination) also cannot be moved because of this.
I have seen that synchronize local / remote can be used for get / put to overwrite files like this. But I could not find a solution to use for the mv command.
I also tried (instead of using the mv command) copying and then deleting the files between the remote folders, but I couldnt find a command for copyi[/code]ng files between remote folders.
Is there a way to solve this?