Notepad++'s line numbering system just counts the lines in order. You cannot trick it as you described.

The Compare Plugin will line things up side-by-side, and it will appear to add more lines while viewed in Compare mode… but as soon as you turn off the compare mode, the original file goes back to the original line number (and when it’s saved to disk, even if you are in Compare mode, it will save the real file, not the one with extra lines).

Alternately, you could start with the original file, and use the column mode selection and Edit > Column Editor dialog to insert line numbers in the text, which will match up with the original line numbers in the document. Then, if you had to insert lines to get things to line up correctly, you will easily see the empty lines as compared to the lines that start with the number. When done, you can delete the blank lines (Edit > Line Operations > Remove Empty Lines), then use column-selection or a regex to remove the numbers at the beginning of each of the lines.