It is very odd that you should lose a villager while the game was paused. Just out of curiosity, what steps did you use to pause and close the game?

We have seen a few reports of dead villagers "going missing" with no grave or other record, but not while the game is paused. We are working on finding the cause of this issue, and I'll add your report to our defect tracking system.

I really don't have a good answer for you at this time.