Edit: So turns out, you don't have to open all the Sanctums there are - just a couple mandatory ones. I managed to get another call with Arlecchino on the Grand Exhibition phone where he asks you if you're a murderer. You can answer whichever way you want and you'll get a box containing the key needed to open to the door to his hideout. Other phones might work too, so just check another phone that is not inaccessible.

Might be a long shot, but I'll make a post anyway. So after progressing through the story enough, you end up back at the beginning of the game at Krat Central Station. You then progress through this area until you come back to the Hotel and continue in Relic of Trismegistus area, thus locking yourself out of the area.

Now, to be able to get the final key needed to get access to the room where Arlecchino is held in the Arche Abbey, you apparently need to have found all the prior Trinity Keys and have opened all their respective Sanctums. One such Sanctum is next to the Krat Central Station Plaza (?) stargazer which is inaccessible by now.

Is there any way to return to it and get the Sanctum? Would suck if I had to postpone the questline to NG++ since I wanted to get this out of the way before starting yet another playthrough.

Thanks!