(sorry for my bad english!)
a baad problem happens for me. I uploaded a big file (~600 MiB) via FTP. After ~3h the upload has finished.. or not.. after it was finished/or in this moment, a error appeared. Something with timeout (sorry, I haven't looked exactly). I clicked "reconnect", and then WinSCP started to overwrite the whole file, whithout a request. Realy bad for me. :(
I used the version 4.1.9 (Build 416).
I hope you could have a look at it..?