If you tell them that you have a problem scanning them they will do them for you.
I had a couple of documents that were faint and I scanned them and made them darker in Photoshop.
I supplied scans of my wife's passport and uploaded them but as I explained in an earlier post they scan it with a special passport scanner when you are called to see the caseworker. Whether the woman deleted my scans or not. I have no idea.
With my wife's passport they only scanned the pages with info on them. The same as I did with mine (not the blank pages) and all was fine.
They don't keep the originals of anything nowadays as they don't stick anything in your passport for FLR or ILR. Obviously a BRP with FLR and I am pretty sure it's the same for ILR.