What is to say the knowledge is destroyed just because the books are?
In hindsight this may be what one of my previous DMs did. In a similar scenario (except we knew the books were headed for someone powerful), we destroyed the books but as we did a strange mist rose up. Didn't think much of it until we all started having strange snippets of dreams. Turns out the knowledge of the spells was transferred to the party, spread out so no single person knew how to cast the apocalyptic spell.
You can bring this in too. Members of the party have a dream where that book opens up for them, flicking through pages and showing each of them separate components of the spell. The next day perhaps they see the king's men interrogating the man they pinned the crime on, perhaps some mages talking about how to extract the knowledge from the man's mind...maybe even suspecting that it isn't him the knowledge has seeped into.
You can then have the party hunted down by the king's men for the information stored in their minds.
In the campaign I was in we would have encounters with a group of mages trying to extract the knowledge from us (taking up their action each turn and we had to make wisdom saving throws) and some others protecting them. It makes for interesting combat.