Well, in the beta the spellbooks weren't actual items, they were abstract. Having access to the Fire book didn't mean you had it in your inventory to be traded away/lost/dropped/etc. But getting them unlocked their respective spells for research.
If they're still not items, then chances are you can't capture them, either (honestly never tried in beta ).
As for Sovereign escaping, each time costs a permanent 1 essence. The AI was dumb about it and kept attacking and losing the lone Sovereign over and over, so hopefully that's better in release, but unless you heavily pump into Essence, it becomes a costly habit.