The immortality part is uncertain: in canon it let Flamel survive for six centuries, but in HPMOR Quirrel claims that the stone's current holder is not the one who made it.)
In canon, the elixir of youth is something you have to make and drink over and over; if the Stone were stolen, and you were unable to make a replacement in time, you would die of old age. It's possible that this is what happened, with Flamel as the thief. This would also explain why he can't make more Stones.
New chapter!
This is a new thread to discuss Eliezer Yudkowsky’s Harry Potter and the Methods of Rationality and anything related to it. This thread is intended for discussing chapter 104.
There is a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author’s Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: