The next version of WinSCP will automatically restore the editor options defaults when changing editor command from Notepad to 3rd party editor
Issue 1872 – Automatically restore external editor defaults when changing editor command from Notepad to 3rd party editor

This can only happen, if you have explicitly enabled External editor opens each file in separate window (process) editor option (or you are using an old version of WinSCP, or you have set up your extenal editor using an old version of WinSCP):
https://winscp.net/eng/docs/ui_editor_preferences
Try to disable the option.

I noticed annoyance. When you edit some file and close it, program does not know that you closed the file.

If you try to open/edit that file on the server again, it will display error:

WinSCP 5.0.5 beta

Thanks