Same thing happened to me, but it was due to the first hatched duck rolling the unhatched eggs. I set everything aright again, and still saw movement in the eggs around 11 pm the same evening that the first egg hatched. By morning, nothing. I'm assuming that after a few minutes of being rolled, they must have gotten enough fluid in their lungs that it compromised them enough that they faded and died overnight.
Sorry for your loss. We ended up with just one as well. I found a person about a half hour away selling ducklings about the same age, so I got a few to keep little Jr. company.