Yeah, I'm sure.
Maybe the problem is because those files are 0k, like they are in the tree but contain nothing and are impossible do delete?
Sorry, I do not follow. First you claim that you are sure that you can delete the file. And then you speculate why you might not be able to delete it.
As I have asked above already – if you can delete the file anyhow (WinSCP GUI, FileZilla, ...) please post log file showing that.