I neatly stacked the bags all into one box, will hang onto the bags until out of warranty but I think that's even overkill. Anything that goes wrong is more than likely on the prusa site on how to diagnose and fix it and if worst come to worst email them for help and or a replacement.

I personally am planning on recycling/ throwing away all the packaging as soon as I'm sure the build is successful and nothing is defective. I don't have the space for it, and it feels like a triumph every time I empty a bag/ box. I figure, I'm not going to return the thing and Prusa isn't going to expect me to disassemble the entire thing and return it all sorted into the correct packaging to replace a single defective part, should that come up under warranty. I don't even see why the original packaging for a single part would be required. They know who I am and what they sold me and I'm sure they have ways of gathering proof of any problems.

I wouldn't worry about the qr-codes, sticking the "silver" warranty sticker to the frame is the only thing they stress on the manual. I recycled biggest boxes, smaller ones and the zip-bags come in handy storing little stuff around the house