Bob could claim e.g. that she escaped after being kidnapped and he's no longer aware of where she is.
Alice's dead body can still be found at some point, which could prove that Bob killed Alice; or she can be found alive, but because of any reason did not want to be found.
By all means, sentence Bob for kidnapping, stick him in jail, have him get out, put a tracker on him and forbid him to leave the country. Then, when Alice pops out and is dead, you just trial him again. It's a different crime! What's more, even if it was the same crime, it'd be material new information!
(Quoth the ECHR: "The provisions of the preceding paragraph shall not prevent the reopening of the case in accordance with the law and penal procedure of the State concerned, if there is evidence of new or newly discovered facts")
You jailed Bob for years for the crime he didn't commit. Are you happy?
Presume Alice was 'kidnapped' in the ball for XX years. You trial Bob and sentence him for 20 years. 20 years passes, Bob serves his sentence and some time later it occurs what Alice were dead all these years, but Bob not only left the country but served his sentence.
Or you sentence Bob for the murder of Alice (even better - execute him), yet Alice is alive, though 20 years later.
Thing is, till the bubble pops you don't know for what exactly you should punish someone and hence - how hard and harsh.
It's a classical dilemma of bringing in/justice with the lack of means to prove anything.
There was a short story in a similar vein with a 'light retarded glass', ie glass what slowed the passage of light through it for times. It were essentially a CCTV/DVR with a years to retrieve 'the record'. The protagonist of the story waited for ~decades waiting to confirm if he sentenced the culprit rightfully for murder or he murdered innocent person with the state authority. Maybe someone would remember what was the name of this story.