That depends on supporting evidence--any witnesses, video cameras, and the number of the ballots discarded. Site security might limit access, too. Aren't ballots indexed with code of some sort which indicates whether they are legit?
I saw a Conspiracy theory that said ballots were printed with an invisible "watermark" that proved the provenience of real ballots, but I don't buy CTs. The ballots themselves are not serialized, they can't be in order to protect the secret ballots. And, any other identifying marks can simply be copied along with the rest of the ballots.
I suppose microprinting, like that used on currency, could work. People can't see them, but a good optical scanner can. The problem with that would be the cost of printing ballots would necessarily skyrocket beyond the means of the several (50) states.