This thread is a year old, but it addresses my problem. I have a rooted Note 3 with KitKat 4.4.2 and it fails to upgrade with 'your device has been modified ...'. My bank is upgrading their mobile app and it won't run on anything older than Lollipop, and I really need the new version because the existing one barely works at all.
I hear that I can upgrade to Lollipop only with Samsung Kies, but Kies is available only for Windows and Mac, and all my PCs have Ubuntu.
I'm pretty stupid about android - I paid someone to root it for me. I suppose I could learn how to do it myself, so I could unroot it (which I also don't know how to do), upgrade to Lollipop, then re-root it.
Suggestions?