Much like in the Buffy wish!verse, Rachel eventually returns to Lima, after having been in foster care almost her whole life, and after running away from an abusive foster home, Shelby takes custody of Rachel. Quinn feels guilty about the wish and all the terrible things that happened to Rachel because of it, and confesses everything to Rachel. Rachel doesn't really believe her, but the two go to Cleveland anyway and get help from Giles who restores them to their original universe, but with their memories of the Wish!verse intact.
The fic was a long, multi-chapter story, and I read it on LJ. I'd appreciate any help finding this fic, because I've been trying and failing to find it for a really long time.
ETA: Found! It's The Wish by sulkygeekff. Thank you!