The box super keeps updating
Leave the device alone to do its thing—that’s just Flash Fire running the needed commands. If you’ve modified your device in a way that prevents Flash Fire from applying the update—maybe you’re running a custom kernel, or the /system partition has been modified by the Xposed Framework, for example—then the update will “fail.” There’s currently no notification that the update wasn’t applied, so you’ll have to jump into the Settings About phone menu and see if the build number has changed.
When it’s finished, it’ll reboot with the update flashed and root restored. If not, then you know the update wasn’t applied (there’s also a good chance Android will notify you that the update still needs to be installed).
Go ahead and tap “OK.” This will generate a screen that may seem a little overwhelming to novice users, but it’s essentially just a breakdown of what Flash Fire intends to do with the OTA file.
Rooting is the process of enabling access to the root account, installing the su binary.
If you can’t get the OTA file, you may be out of luck.
Furthermore, if you’re running a rooted device that’s getting a full version update—from Lollipop to Marshmallow, for example—things get murkier.
On Lollipop and earlier versions of Android, the over-the-air (OTA) update sets your Android system partition back to its factory state, removing the su binary.
On newer devices with systemless root, it overwrites the boot image.