I assume you are not able to reproduce this problem easily, right?
Without a verbose session log file, it's hard to tell for sure, if this is client or server log file. But to be honest, I doubt this is WinSCP problem.
5.15.2 Build 9590
3rd time 3 diff versions in idk how many years
W7, W10, x64
Simple copy everything looks fine in the logs on both ends.
Just copied the files for a project by accident from the mounted drive of a samba share to the same location connected via sftp and all the files got nulled. They occupy the same space just their contents are all zeros.
Not actually sure that this is a bug I'm just here trying to make notice of it, and I believe that there are more skilled people here to explain this bug of an idiot kind of issue :)