Can I release an update to the app store with "Build Active Architecture Only" set to "Yes"?

If choose "Build active architecture only" YES, it will speed up your building time, by build only current architecture. But when you build for release, please set it to NO

This link may help you...

http://useyourloaf.com/blog/2010/04/21/xcode-build-active-architecture-only.html

However, I have built some apps previously and submitted them to the App Store with the option set. This was due to me having an older iPod device that I used for 'Archiving' the app and the subsequent submission, whereas the build target included ARM7. Without the option set I couldn't build it for the older iPod and thus couldn't archive and publish.

So, I would say from this that you will be fine, without going through the pain of resubmitting and subjecting yourself to a restarted counter waiting for review.

Mark