Yes, seems like it will count as a late app. We submitted ours earlier today, and the messaging on http://news.ycombinator.com/apply now reads:

"The application deadline for this cycle has passed. You can still submit a late application, though the chances of getting funded are lower.

<link>apply late</link>"

Was this your first submission or update to the old one?

hmm.... I guess the "fair" thing would be for it to count as late, although I wish that wasn't the case.

I struggled to figure out what the "hack a system to your advantage" question really meant (given that I read that pg essay a while back on what "hacking" "really" means, although the question seemed to be referring to the other meaning contextually) and now I found out that I was wrong......

Could've had a pretty good answer for it, too. ho-hum.