I think so. The way he tosses it away like an item suggests to me it's just like that - when you use up a Super Scope, for example, it doesn't recharge, it's just gone. Not that I'm saying it's impossible, of course - pure speculation on my part.
Either way, pretty sure your specials will be unusable until you get that Tome back (by whatever means). Or at least severely gimped.
She also releases an Arcthunder near the end without charging, either; I'm assuming you can hold the charge, though it is strange there's no visual indication of her holding a Thoron.
Perhaps it could be similar to resummoning Pikmin, but with a longer charge? I can't imagine it gimping the character for an entire stock; that'd be lunacy on par with tripping.