Solved it locally at first: unzipped the pez file, searched for the smallest objects, and scaled them up. It might look a bit funny (that ball which had been made much smaller would have been scaled up), but people could again fix it using the prezi editor.
Used this manually to ‘fix’ other peoples presentations, in which they send me their pez file, I would ‘solve’ it and send it back (usually: they would invite me to be a co-author, I would make a copy, fix that and make them editor to that copy). Used to do this quite a lot on the prezi forum.
In the end automated it completely: made a service in which one could upload a pez file, my NAS would decompress it, fix is, compress it again, and mail a link to the corrected pez file.
Software is defunct as problems have disappeared (and changes to prezi way made it no longer work).
Incidentally not my first prezi product: I guess that was the Android app that made it possible to view a prezi on an Android phone or tablet, ways before Prezi themselves made the Android app (I think they already had the iOs app, not sure). [That app ran in more then 50 countries, but that is another tale;-0]