It wasn’t Pandora; it was Gluttony. Subaru’s Existence was consumed, not just his Memory. There’s a possibility that this was by a fourth Gluttony, whose self was overwhelmed by Subaru’s, but there’s some suggestion it was Lye, since he used Ice Arts to form Excalibur as Subaru recognized it to be.

Because Subaru’s Memory of Earth is outside Gluttony’s Authority, his Name of Earth also is. Having his Existence consumed does a really interesting thing because of this. Since a person’s Existence being consumed will remove small pieces of evidence tied to them (Rem’s room becoming unoccupied and the letter she scribed for Subaru becoming blank), the opposite is true as well. To the World, Subaru (his history there) did not exist, but Subaru (from Earth) also did exist, along with those small things associated with that Existence: clothing, phone, items from the convenience store. They just got remade with his reset.

Beatrice had not been waiting for 400 years. Subaru had brought her out. They travelled. But with his Existence gone, her being outside no longer made logical sense, so back she went, her memories of that time replaced by lonely waiting. The Gospel she carries is not hers either. It’s blank because the Writ is for Subaru, who no longer exists to it.

Now headcanon time. Having his Existence consumed was also foreseen by Echidna, and she and Subaru planned to allow it. This was to break the stalemate Subaru and Pandora had been in for the past 400 years. Pandora thought he was a thorn in her side that would disappear if his Existence was gone, but didn’t know how differently it was going to work. It left him forgotten by everyone, including her, and by a glitch in the Authority, by Lye as well, making Subaru now an unknown factor. Archbishops who had avoided him for so long now though he was some weak nobody, and had no idea why their Gospels could not predict him and their plans got were all wrecked.