KOReader on Aura One & Patches

I bought an Aura One almost the day they were released, so have much experience there, but none with KOReader, although I would like to experiment with its PDF display.

My question: My Aura One is heavily patched, because I like to fiddle so much with the screen display. If I install KOReader, do those patches still persist when I'm in Nickel? What worries me is that it looks like I replace a key file to get KOReader installed, and am not sure whether I would be abandoning my patches or not.

Thanks for any information.

Paul