If you have a slow/choppy internet connection, it's common that during a conversion of a large number of comments to nodes you'll get a warning and the conversion won't work. I don't know what the warning was because I can't reproduce it now (my internet comes and goes). If this happens, as it did in my case, the conversion won't work, but node comment will still think you're using nodes as comments, so it will basically just seem like all your comments have been deleted because it will use the node comments but won't find any to display.

However, they haven't actually been deleted, and to reverse this simply change your settings back to the default drupal comments. This will revert things back to normal and you'll see your old comments on the node type again. You can now go back and change them to your node comments and, assuming your connection works now, it will run the conversion successfully.

Just a heads up.