Replace your script with WinSCP .NET assembly code:
https://winscp.net/eng/docs/library_from_script
Use Session.SynchronizeDirectories:
https://winscp.net/eng/docs/library_session_synchronizedirectories
Iterate returned SynchronizationResult.Uploads and create/upload a flag file for each.

Hi, Thanks for replying. Yes, Each file needs to have a flag file and they can be written all at once at the end of the synchronisation if its easier to to it that way?

So you need to write the flag file for every single synchronized file? Or just one flag file after whole synchronization is done? Or if separate flag files are needed, can you write them all at once after the synchronization completes?

Hi,

I wonder if anyone can help, new to winscp. I am trying to sync local folder to remote folder and when file is complete create a file flag like txt file to let the other side know that it is complete. They have automated scripts that check this on their side so have to comply with this requirement but I don't know where to start?

If the file transfer fails then it doesn't write the file, any help appreciated.

Thanks