Heads-up: there's been a code upgrade to the FO3 Nexus. I was checking over RR the other morning, and the comments thread wasn't attached to the file anymore. Hit my files listing and almost half of them had the same problem. I've filed a bug report, so hopefully they'll be back soon.
If you have any files on the FO3 Nexus, you might want to check it out and make sure everything is still as it should be.