This is highly annoying. One assurance I thought I had was the porting of Disqus comments over to the new site would be no big deal. The URLs were the same, so it should be a breeze!
When you start a post in Drupal, the default URL is node/[node id]. The generation of the "pretty" URL doesn't happen until the post is previewed or saved. Therefore, if you happen to be on node ID 10 and preview your post, Disqus assigns the thread ID as /node/10, and the yet-to-be-determined URL (in our case, generated from the post title) is irrelevant. The node IDs from the old site aren't the same node IDs on the new site, even though the URLs are exactly the same.
That in itself is no big deal if there's a way to remap the old IDs to the new IDs. They have instructions on how to accomplish this, but it didn't work. Just getting to that option was difficult because the navigation in the instructions, updated as recently as a few weeks ago, were completely different than the actual navigation. I was able to download the old URLs in CSV, assign the new URLs, and upload the new list faster than I was able to even find where to do it.
In the end, we said screw it and are starting from a clean slate.