Try to set longer [pm]Session.Timeout[/m].
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For one time we can upgrade and restart but restarting is not a great solution because it production box and we can't restart it during business hours.
Which version has this fix?
Do upgrade will make sure it will not occur again?
Which latest stable version should I use?
This is a known bug in older versions of WinSCP:
Please upgrade and restart you server.