() while chomp $line;

That would only work if $/ happens to match whatever is at the end of the line. If it really is just a matter of one or more "\n" with no preceding "\r", then you would do:

  s/(?<!\r)\n+//g;  # should probably leave "\r\n" as-is
[download]

which would work no matter what $/ happens to be.

As for notepad.exe displaying a box to represent "\n" when it is not preceded by "\r", that's an interesting point that I was not aware of. But I would still expect that it also uses the box to represent other code points for which the current font does not have a defined glyph -- in other words, the box is ambiguous: there might be a variety of different byte values (code points) that would cause it to appear.

And yes, notepad.exe is a display tool, in the sense that it makes data visible to the user. But since it's also a text editor, it makes certain assumptions about what the user is interested in seeing. (And the same goes for wordpad.exe)