Unfortunately it doesn’t help you with your current data loss, but there is now at least a partial safety measure taken for this situation in the upcoming v8.9.3 - for the case of a modified file, that Reload-dialog offered default answer has been changed from YES to NO:

npp-safer-reload-default-for-dirty-files.png

For unmodified files, the default remains YES.

Hi @JAK ,

You can use ComparePlus but from the menu choose Find Unique Lines command. It will mark all unique lines in a file (that are not found in the other file).
Then use Diff Visual Filters... to hide all diffs (this will hide all unique lines). Don’t worry if there is still one visible diff line on top - first document line cannot be hidden but it is not a problem for the next operation.
Then select the file from which you’d like to remove duplicating lines (set the focus/caret in that file) and execute Delete all/selected visible lines from the ComparePlus plugin menu.
This will do what you are trying to accomplish.

BR