This usually has nothing to do with WinSCP. It is typically caused by the FTP/SFTP server.
- The server may automatically move away the uploaded file for processing.
- Or the server may move away uploaded file after processing it. In this case, you may sill see the most recently uploaded files in the remote directory, but not the files uploaded earlier.
- Or the server may rename the uploaded file after processing it, to mark it as processed.