Well, I mean there's always the possibility that you'll have users that won't log in any time soon, and you don't want them to be vulnerable in the mean time, right?
If it were me doing it, I'd take the article's approach as the first whack, and then as each user logs in, validate their password (as per the article), and then also set their password to scrypt('salt', 'password') vs. scrypt('salt', md5('password')), so that they were current. Then just set a flag on the user record like "new_password=True" or something.
That gets you the stopgap without having to muck around with scrypted hashes forever. Send out a few emails to your user population with a note that you've upgraded your password strategy and that they should log in. You're still not going to get 100% coverage, but at least for whoever you don't get to log in, their passwords aren't 'in the wind', so to speak.
Edit: I'm not sure if you edited yours, or if I just read it poorly, but I think we're saying the same thing. Note, the article's strategy is basically your first scenario -- just bcrypting (or scrypting in the article) the existing md5 hash.
If it were me doing it, I'd take the article's approach as the first whack, and then as each user logs in, validate their password (as per the article), and then also set their password to scrypt('salt', 'password') vs. scrypt('salt', md5('password')), so that they were current. Then just set a flag on the user record like "new_password=True" or something.
That gets you the stopgap without having to muck around with scrypted hashes forever. Send out a few emails to your user population with a note that you've upgraded your password strategy and that they should log in. You're still not going to get 100% coverage, but at least for whoever you don't get to log in, their passwords aren't 'in the wind', so to speak.
Edit: I'm not sure if you edited yours, or if I just read it poorly, but I think we're saying the same thing. Note, the article's strategy is basically your first scenario -- just bcrypting (or scrypting in the article) the existing md5 hash.