I'm posting my solution from the other thread, too (moderators, merge if you wish):
After my 2.5.1 upgrade, my feed also stopped working.
At Feedburner, my feed was pointing to "mysite.com/wp-atom.php" and it started coming up blank. While testing and trying to solve, I noticed "mysite.com/wp-rss2.php" was blank too. So, as you say above, they've apparently been depreciated in this release (thanks for the heads up, folks!) ;)
Here is how I solved it:
1. Deactivate Feedsmith Plugin
2. Log into Feedburner.
3. Choose "Edit Feed Details"
4. Where it says "original feed", put: "http://www.yoursite.com/feed" (DO NOT USE A TRAILING SLASH!*)
5. Save feed details
6. Go to the "troubleshootize" tab. Choose "Resync" [Don't know if this is necessary but I did it anyway.]
7. Go back to your WordPress admin page and turn the Feedsmith plugin back on
These are the steps I took tonight and it APPEARS all is normal again.
* - This (trailing slash issue) had me ripping my hair out because (in my case anyway) with a trailing slash in place, it was being redirected to Feedburner's own blank feed - so Feedburner was essentially checking itself for content instead of my actual feed.