The next version of WinSCP will automatically restore the editor options defaults when changing editor command from Notepad to 3rd party editor
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Sorry to bump this, but to add additional useful information:
Even with the "External editor opens each file in separate window" unselected, you still need to modify the editor command line to tell EditPlus to use an existing process (-e) to load additional files in. Otherwise it will still open in separate windows (because of editplus, not winscp). Having forgotten this on every install I've done and then having to redig the option, I finally just updated the https://winscp.net/eng/docs/ui_editor_preferences page to reflect this information (since this web page is the first google answer).