Resetting passwords programmatically fails

I’ve imported users into a BuddyPress/Multisite install of 3.9.1, but have a problem:

I can change users’ passwords via the admin interface and that works fine. I use MD5 to update users via phpMyAdmin and get a different hash as a result and users cannot log in. The Codex says that this should work. There are over 200k users, so manually resetting them all is not going to happen. I don’t want to set them to the same password because naughty people will take control of others’ accounts.

It seems to me I might be missing a trigger function on wp_users or something like that which provides the ‘double hash’ mentioned in the Codex. Anyone know if that exists? Or perhaps a way to use PHP to generate the ‘double hash’ that the Codex speaks of?