Nicholas did not tell Perenelle, about what the Headmaster had done. He had checked, as the magic of the stone was from his mother and house elves. He bought more elves, especially old ones from families for more than they normally are worth.
He was lucky in that he found five Potter elves for sale. The younger three would be needed later. So they had thirty nine elves. He would need twenty three for the stone. It takes ten to keep everything going, leaving six for child raising, elf and human. Three elves were pregnant. So three to take care of Perenelle and hopefully Harry. He had checked out Harry's living conditions and could not believe that Albus had become evil. He freed Fawkes from the binding. Just asked her to keep an eye on Harry. He enchanted a small stone that would make it seem, she was still bound to Albus. Each burning day (once each year) she would reswallow the stone.
He created a new stone with the elves and his life. He had been using a glamour and having Perenelle to become younger. He wanted her to be Harry's mate when he was gone. He left Harry a number of letters for different times he aged. Twelve, thirteen, ectextra. His first letter to Perenelle started: Albus Betrayed Us, My Love!
