I mean thing is this type of issue has already been addressed with other mons. Did you not notice that Jirachi had a location despite only being available via trade? This was a question asked before Hoenn and the solution was to take a location that was un-occupied and place her there.
Another example is actually in this upcoming update. Dialga and Palkia both appear at the sky pillar with Arceus above it while the lake trio have individual lakes. This is an issue because some legends are too clumped while others who don't need to separate are. Chainsaw's solution as I remember it being confirmed to me was to move the lake trio to Lake Verity which is close to Dawns home town thus drawing the pairing (Dawn is paired with the lake trio if you didn't know). Because they are all at Verity, the two other lakes become open so move Dialga and Palkia to those lakes, keep Arceus at the sky pillar bada bing bada boom you got the legends were they are narratively best placed.
So something like that can be done for Enamorus because there is a lot of fun narrative potential there. Have the other genies clearly indicate missing their dear sister and how she's ran away somewhere else after a fight or something. You could make it darker and have it be implied she's straight up extinct already BUT because you will have Dialga with you, you go back in time to the times of Legends Arceus and bring her to the future. I doubt it will be dark like that but you could have a compelling little narrative between the 4.... also a scene where they fill each of her holes that kinda writes itself.