Here in 2015 iCloud is still muddled. My Keynote was probably too big for it to track properly. So I move the file to a local folder on my Mac - Documents; but any folder is fine - let the iPhone Keynote remove the file, then move the file back into the Mac's Keynote - iCloud file. Then iPhone Keynote will download the presentation as a new file.
I think the file on my iPhone gets corrupted or something. This painlessly and safely deletes it and lets you start over.
Also: get off your telco network and use you WiFi for this. I noticed a real difference in speed. I suspect Apple made some kind of deal with them.