There are separate passcodes for the phone and for iCloud. An iOS device will automatically sync a backup to iCloud once a day if iCloud backups are enabled provided the phone is connected to power and a wifi network. When you first enable iCloud, the phone requests your iCloud password and stores it. If you change your iCloud password, automatic syncing is disabled until you unlock the phone and enter your new iCloud password there.
The FBI cannot unlock the phone. By changing the iCloud password, they have made it so that the phone cannot even possibly sync without first being unlocked. Knowing the iCloud password is of no utility for them.
