Luckily, I caught this advisory from Bootswatch about Bootstrap 3.
At some point they're going to switch over to Bootstrap 3 themes in place of the current Bootstrap 2 themes. This is good -- at some point we will probably switch Fargo over to Bootstrap 3 as well. But we will probably always want to have a snapshot of their version 2 themes around, so I just made copies of them and made a change to the core Trex code to generate URLs to our copies instead of theirs. This was always the fair thing to do, there's no reason they should be paying to host files that we're using for our sites, esp since I'm now using a Bootswatch theme for Scripting News.
Trex now changes all bootstrapTheme URLs that point to bootswatch.com to point to the location on smallpicture.com where we're keeping copies of the themes. So there's nothing you have to do to use the copies, that's automatic.
It's probably safer, long-term, to use the name instead of the URL.
But for now, either way works.