Earlier quoted context omitted.
It's one way to do it, which is okay sometimes. The other way is to add a new empty column for bcrypt. The next time the user logs in, you save the bcrypt hash and you remove the MD5 hash. Over time, the active users will be migrated to the new scheme. The only issue is the abandoned accounts, they'll keep the old weak scheme.
There are other migration techniques. If you know md5(password), you can create bcrypt(md5(password)).
Usually you do this by decorating the bcrypt(md5(p)) entries in some way so you can recognize which ones are tested with bcrypt() vs bcrypt(md5()).