May have found a solution. So far successfully editted 10-out of-10 with by changing Notepad++ to multi-instance mode.
Settings > Preferences > Multi-Instance > Always in Multi-instance Mode
Note: You MUST restart Notepad++ for this setting to take affect.
You should have this behavior, only if you have "External editor opens each file in separate window (process)" enabled in your configuration of Notepad++ in WinSCP. The option is NOT enabled by default.