I basically planned a scence just like that already, but as the intro to Enamorus's section, the other 3 Genies would ecplain how their Sister vanished over a century ago and they assume she's dead.
Dialga and Palkia work to send the MC back to Hisui so he can look for her.
I might make Enamorus a 1 attempt Mon like the Mythicals, explaining that repeated Time Travel is too dangerous (obviously save scumming will still be a thing)