When transferring a file, WinSCP checks to see if a file of the same name already exists, and if it does offers a dialog box with a variety of options, including "New name".
If I choose the "New name" option, and enter a new name for the file, WinSCP does not check to see if a file of the new name also exists.
This seems like an important omission. I have at least once lost a file I didn't want to lose because my finger slipped and I submitted a "new name" that was identical to the old one. I can also imagine a situation where I did enter a new name that was inadvertantly the same as another file I also didn't want to lose.