I edited a bunch of PHP files (with N++) on Computer A, uploaded it to a server, downloaded it to computer B (with N++), and they lost all their line breaks. I've done this routine many times and never had this problem.
I've tried
There seems to be a question missing?
If you want to format it, you might just want to let a code-editor that knows indentation (auto-formatting) fix it for you. Eclipse can, I'm sure netbeans can too. I think eclipse auto-formats everything you paste automagically, but otherwise just find the formatting commands ;)