It's probably that the server ran without Mystcraft being installed, and therefore removed the Mystcraft books as it didn't know what they were, though I'm not sure. Do you have a backup of the server? You may be able to restore from a backup then update the server, and install Mystcraft before starting the server after the update. No idea if this would work, but worth a shot. Otherwise you may need to /tpx to the various Mystcraft ages and create new link books.