So you keep WinSCP open all those "few hours, days or weeks"?
Yes, I don't close it, since it's on VPS, I'm fine with it.
And you do not update those files. But WinSCP suddenly starts trying to upload the file, as if they had been changed. And it fails to upload them, as they are in that strange locked state. As that correct?
When this problem occurs some files could be updated during last 1-2 days, other files could be edited very long time ago, and in both cases files could be opened in editor or closed=not opened anywhere except WinSCP trying to access them, while nobody asks to do it. I think WinSCP is not trying to upload them, just access.
Most of time this problem happens not when I'm using VPS, so I can't guess more why it happens. After night I'm connecting to VPS and sometimes I see this. Once in a week maybe.