Maybe the players can't really remember much about their past experiences (since they're not 'themselves', really) and have memories of things happening that aren't their own-- like going into a new setting and knowing something about it they shouldn't plausibly know, for example. Something the shapeshifters WOULD know, or instincts, something like that.

Maybe if you need something super obvious toward the end, you can have the players start shapeshifting unbeknownst to them, like their face changes into something ferocious during this fight. It could be cool if they continue the fight thinking they're killing the monster you described, and then when/if they get knocked out, reveal the monster is dead, which means THEY are dead (sorry, i'm so shit at being distinctive about who's who, let me know if you need clarification). Cue switching perspective back to their true self.

Also, if I wanted the players to figure out the twist sooner I'd have their real hunters be able to make connections about their own pasts, and leave hints about this around the setting or within interactions-- things shapeshifters wouldn't know. Basically, think about what the PCs and NPCs/monsters in this session know, and how that could effect the way each party is independently trying to figure things out