Please attach a full session log file showing the problem (using the latest version of WinSCP).
To generate the session log file, enable logging
, log in to your server and do the operation and only the operation that causes the error. Submit the log with your post as an attachment. Note that passwords and passphrases not stored in the log. You may want to remove other data you consider sensitive though, such as host names, IP addresses, account names or file names (unless they are relevant to the problem). If you do not want to post the log publicly, you can mark the attachment as private.
Though I'm pretty sure this has nothing to do with WinSCP.
Isn't it rather that the server processes a file after it is uploaded and removes it from the folder?
And it's only after you upload another file that WinSCP refreshes the folder and finds out the previous file is not there anymore?
Can you try to refresh the folder manually shortly after an upload to check if the uploaded file indeed disappears?