Older stories are still around. They're just not linked to anymore. You can search for them at nycs.bigheadlabs.com
You must have an API that gets you access to these unlinked posts, correct?
while True:
i += 1
if not urlfetch('http://news.ycombinator.com/comments?id=%d' % i):
break
# implementaton of urlfetch() left as an exercise to the reader
Older stories are still around. They're just not linked to anymore. You can search for them at nycs.bigheadlabs.com