Encrypt existing unencrypted Time Capsule backup

Unfortunately Warren didn't post as an answer but as a comment; I can't emphasise enough that he's totally correct.

Removing/changing one file won't fix your REAL problem; it will make ONE symptom go away. Take the box offline, take an image for later forensics, and re-install, with a newer version (hopefully w/ new security fixes) of whatever you were running.

I repeat: deleting the file is NOT A FIX.

Sorry I didn't do more digging before asking this, but going to answer my own question in case someone else finds this.

I've taken a look inside the user_save function, and seen that it does some invoking, so I did it too. Surprise: it worked (EntityCache was the bad guy who was caching everything BTW).

Here's my code for reference:

$usr->field_somefield[LANGUAGE_NONE][0]['value'] = 0;
field_attach_presave('user', $usr);
module_invoke_all('entity_presave', $usr, 'user');
module_invoke_all('entity_update', $usr, 'user');
field_attach_update('user', $usr);